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revision 1.403 by heimbach, Sat Dec 4 23:26:49 2004 UTC revision 1.2351 by mmazloff, Sat Sep 2 22:25:46 2017 UTC
# Line 1  Line 1 
1  $Header$  $Header$
2    $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/bling:
8      - bling_production: Fix typo in calcium carbonate uptake. Also rearranging and cleaning
9    o model/src:
10      - move k loop inside correction_step.F (+ update calling S/R)
11      - collect implicit pressure gradient tendencies in local 2-D array;
12        affect results (at machine truncation level) when using 3-D solver; update
13        output of exp.: exp4 (x1), global_ocean.cs32x15 (x2),hs94.cs-32x32x5.impIGW,
14                        rotating_tank, short_surf_wave,tutorial_deep_convection (x2)
15                        & tutorial_plume_on_slope.
16    
17    checkpoint66j (2017/08/15)
18    o pkg/ptracers:
19      - fix surface forcing under ice-shelf (useShelfIce=T).
20    o pkg/atm_phys:
21      - use hFac weighted average when applying A-grid atm-phys momentum tendency
22        to C-grid dynamics; this ensures wind-stress match mom tendency.
23    o eesupp/src:
24      - change default for opening scratch files to avoid STATUS='SCRATCH'
25      - close scratch files with STATUS='DELETE'
26      - changes affect eeset_parms.F and open_copy_data_file.F and many routines
27        that read namelists (because they close the scratch files)
28      - you can revert to old default by setting USE_FORTRAN_SCRATCH_FILES
29        in CPP_EEOPTIONS.h (tested in ideal_2D_oce/code & lab_sea/code_ad)
30    o pkg/atm_phys:
31      - fix unset arguments in (unused) S/R surface_flux_0d.
32    o eesupp/src:
33      - add argument "procId" to S/R EESET_PARMS to fix  scratchFile1 & 2 setting
34        (case TARGET_BGL or TARGET_CRAYXT) for early call (from eeboot_minimal.F):
35        called with myProcId in eeboot.F and with mpiMyWId in eeboot_minimal.F
36    o pkg/streamice:
37      - remove blank between _EXCH_XY_RL and "()", which my Apple Xcode
38        preprocessor /usr/bin/cpp cannot interpret; 3 instances in total in
39        streamice_driving_stress_fd.F and streamice_advect_2dtracer.F
40    o pkg/diagnostics:
41      - new option to allow to cumulate thickness-factor (hFac) weighted field
42        (if field permitted); implemented by changing sign of "jdiag" pointer
43        (> 0: cumlulate field, < 0: cumulate hFac weighted field).
44        a) restricted to 3-d (Nr levels), level centered diagnostics at U,V or Cell
45           center position (gcode(2)='U','V','M' & gcode(3,5,9:10)='R',' ','MR')
46        b) for now, activated by setting fileFlags 3rd character to 'h'.
47    
48    checkpoint66i (2017/07/18)
49    o pkg/cheapaml:
50      - add parameter "useRelativeWind", default set to False; this change the
51        previous setting which was always using relative wind.
52    o add hooks for the Parallel Data Assimilation Framework PDAF
53        (http://pdaf.awi.de/) in eeboot_minimal.F and the_main_loop.F;
54        to use set CPP-flag USE_PDAF in CPP_EEOPTIONS.h
55    o pkg/exf:
56      - interpolation of vector fields (exf_interp_uv.F): fix bug in calculation
57        of South-Pole mean value.  
58      - interpolation near the poles, case where second additional row is at the
59        pole (or beyond the pole and moved to the pole): change first addition row
60        value to a linear interpolation between pole and 1rst (S.pole)/last (N.pole)
61        row (instead of just a copy of it).
62    o pkg/seaice:
63      - prevent JFNK and KRYLOV solvers from trying to reduce a residual of 0
64      - add the option to compute no-slip du/dy, dv/dx (i.e.
65        the offdiagonal strain rate e12) by a second order approximation
66        on the boundary; works only with JFNK, KRYLOV, or EVP solvers, because
67        it is too messy to implement for the implicit LSR matrix.
68        SEAICE_2ndOrderBC = .FALSE. by default
69    
70    checkpoint66h (2017/06/02)
71    o pkg/seaice:
72      - add new routines to compute stress tensor components and stress tensor
73        divergence to be reused in s/r seaice_lsr and s/r seaice_calc_lhs
74      - change names of diagnostics SIsigI/II (commonly used for invariants)
75        to SIsig1/sig2 (more common for principal components) to avoid confusion
76    o pkf/exf:
77      - add a stop if useRelativeWind with un-updated uwind/vwind (e.g., constant);
78        similarly, stop if rotateStressOnAgrid with constant wind-stress.
79    o pkg/seaice:
80      - remove (comment out) diagnostics SIuwind,SIvwind,SIfu,SIfv (duplicate of
81        EXFuwind,EXFvwind,oceTAUX,oceTAUY) and point them to their equivalent.
82      - add diagnostics of wind-stress over seaice (SItaux,SItauy) and seaice
83        fraction weighted wind stress over ocean+seaice (SIatmTx,SIatmTy).
84    o pkg/diagnostics:
85      - small piece of code to rename (old) diagnostics, when namelist is processed.
86    o model/src:
87      - new run-time param (useMin4hFacEdges) to select method for setting hFacW,S:
88        originally, set as minimum of adjacent hFacC factor ; now (new default)
89        computed from rSurfW,S and rLowW,S by applying same rules as for hFacC.
90        Only matters when useShelfIce=T with particular ice-shelf cavity geometry.
91    o pkg/seaice:
92      - add momemtum advection, off by default, still in test phase
93        most of the momentum advection code is adapted and reused from mom_vecinv
94    o pkg/mom_vecinv:
95      - pass these runtime flags:
96        selectVortScheme, highOrderVorticity, upwindVorticity, useJamartMomAdv
97        as formal parameters to s/r mom_vi_u/v_coriolis, mom_vi_u/v_coriolis_c4,
98        so that these routines can also be used in pkg/seaice.
99    
100    checkpoint66g (2017/04/24)
101    o model/src:
102      - more robust ordering of column thickness integral (=Sum_k(drF*hFac) )
103        to get same expression (regarding machine truncation) in different places
104        in ini_masks_etc.F (e.g., rSurfC,W,S is now exactly zero when it should).
105        Update forward output of experiments: global_ocean.cs32x15 (all 5 except
106        viscA4), isomip (x3), tutorial_global_oce_in_p & tutorial_plume_on_slope.
107    o pkg/shelfice:
108      - ALLOW_SHIFWFLX_CONTROL: move setting of maskSHI from shelfice_update_masks.F
109        to shelfice_init_fixed.F
110      - change S/R SHELFICE_UPDATE_MASKS to SHELFICE_INIT_DEPTHS (still called from
111        ini_masks_etc.F for now) to update ocean upper boundary position according
112        to ice-shelf topography (instead of directly updating hFacC).
113    o model/src:
114      - move call to CTRL_INIT & CTRL_ADMTLM from the middle to the bottom of
115        packages_init_fixed.F to allow other pkgs to set mask and weight fields.
116    
117    checkpoint66f (2017/04/06)
118    o model/src:
119      - add specific run-time param to select level of printed plot-field-maps,
120        set by default to debugLevel. Remove internal param "printDomain".
121    o pkg/seaice:
122      - add flag to add snow mass to seaiceMassC/U/V, the default is
123        SEAICEaddSnowMass=.FALSE., not to change previous results
124    o pkg/bling
125      - Bug fix in bling_production regarding unit conversion for diagnostics
126        being put in the wrong place
127    o model/src:
128      - add back recomputation of rSurfW & S to ensure consistent column thickness
129        (needed for rStar) between Sum_k(hFac*drF) and rSurf-rLow, for now only
130        when using pkg/shelfice; was initially added on 2012/06/01 (ini_masks_etc.F
131        revision 1.51) but was removed accidentally on 2014/02/08 (v1.53).
132    o pkg/autodiff:
133      - clean-up "checkpoint.flow"
134    o pkg/rw (Contribution from Jody Klymak):
135        option to set mds file suffix as function of time in simulation:
136        *) new input parameter "rwSuffixType" (read from PARM03 namelist)
137           to select file suffix format; by default (=0), use iteration number;
138        *) add simple routine to return file suffix according to rwSuffixType;
139        *) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice),
140           use new S/R to get file suffix, except for debug output file (diagFreq)
141           and pkgs offline & rbcs input files.
142    o pkg/rw:
143      - uniform processing of "I10" suffix across writing fld routines; used to
144        simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F
145        (similar to cg3d.F, cg3d_ex0.F)
146    o pkg/mom_vecinv:
147      - highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted
148        vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp).
149    o pkg/bling:
150      - Many small changes intended to clean the code.
151        Unnecessary ADJOINT_SAFEs removed ;
152        removed BLING_COST.h BLING_CTRL.h bling_cost.F ;
153        diagnostics added.
154    
155    checkpoint66e (2017/03/14)
156    o pkg/exf:
157      - interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size
158        definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h;
159        use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to
160        avoid any dynamic allocation ;
161      - S/R EXF_CHECK: add new check & stop when file-name is defined but not
162        read-in ; add warning when file is read-in but not used within pkg/exf ;
163        + check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC).
164      - update exf_summary.F (print {FLD}RepCycle).
165    o verification/global_with_exf:
166      - switch on exf interpolation in AD test (just like the forward test)
167    o pkg/mom_vecinv:
168      - add storage directives to avoid recomputations within mom_vecinv.F
169        which were generating seg. fault with gfortran -devel
170    o pkg/ctrl, pkg/smooth:
171      - initialize array halos which were generating seg. fault with
172        gfortran -devel in adjoint mode
173    o pkg/exf:
174      - for each input field, enable to specify a field specific repeat-cycle
175        ({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod".
176    o verification/lab_sea:
177      - update AD results of primary test and noseaicedyn test after switching
178        to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient
179        check stays about the same.
180    o pkg/exf:
181      - fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T.
182      - exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat
183    o pkg/bling, USE_EXFCO2 code:
184      - add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default);
185      - update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD).
186    o pkg/exf:
187      - rename S/R EXF_INIT to EXF_INIT_VARIA ;
188      - add arguments: fldName (for debug msg) and fldRepeatCycle (set to
189        repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD)
190        and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ;
191      - add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed
192        EXF_INIT_FLD) and update calls in exf_init_varia.F
193      - For now, for backward compatibility, keep a simplified version of S/Rs
194        EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F
195      - add and pass new arguments: fldName (for debug msg) and fldRepeatCycle
196        to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F
197    o tools/genmake2:
198      - replace "bc -l" (only used once) by "expr" (already used).
199    o verification/global_ocean.cs32x15:
200      - turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn".
201        Note: exf setting (data.exf) can be compared to other exf secondary exp
202        "seaice" (kept with useCAL=T) which has same time dependent forcing.
203    
204    checkpoint66d (2017/02/13)
205    o pkg/exf:
206      - remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning
207        early on (in packages_boot.F) to stress this change in pkg setting.
208      - In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg
209    o model/src:
210      - move call to ecco_phys to end of time step; this may induce minor
211        cost function changes by shifting time averages by one time step
212        for some variables; this revision resulted in changed adjoint results
213        in MITgcm_contrib/verification_other/global_oce_cs32
214    o pkg/exf:
215      - Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ;
216        this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields,
217        e.g. precip, are not available.
218    o pkg/flt:
219      - flt_init_varia.F: use pickupSuff if specified
220      - add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first,
221        intermediate, step towards completing pkg/exch2 support within pkg/flt;
222        ifdef DEVEL_FLT_EXCH2 then:
223        - flt_init_fixed.F: comment out stop
224        - flt_exch2.F: conserve ipart, jpart (grid coordinates)
225        - exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates)
226        - flt_mapping.F: attempt to fix longitude diagnostic near date-line
227        - flt_init_varia.F: hack initialization (for testing purposes w. LLC90)
228    o tools/genmake2 & pkg/pkg_depend:
229      - define new type of pkg dependency rule ("=pkg_x"), less strict than
230        the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled
231        (-pkg_x in packages.conf).
232      - change pkg/exf dependency rule from "exf +cal" to "exf =cal";
233      - add "+cal" to dependency list of pkg/ecco (needed to compile).
234      - simplify FWD experiment "offline_exf_seaice" by removing pkg/cal.
235    o utils/matlab:
236      - adding ocean_basin routines for defining basin masks.
237    o pkg/exf:
238      - new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more
239        arguments, allowing to check (and stop) if parameter setting of
240         {FLD}startdate1 & date2 and of {FLD}StartTime are consistent with
241        useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START
242        for backward compatibility.
243      - change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in
244        exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field).
245    o pkg/bling (USE_EXFCO2 code):
246      - fix missing setting of apco2StartTime according to apco2startdate1 & date2
247        by adding a call to S/R EXF_GETFFIELD_START.
248    o pkg/exf:
249      - allows to compile without pkg/cal (but disabled by current dependency
250        rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to
251        run with useCAL=F ; this involves setting directly {FLD}StartTime instead
252        of {FLD}startdate1 & date2 ; consistency check not yet coded.
253    o verification/global_ocean.cs32x15:
254      - fix all data.exf for a shift of 1 day in all field startdate1 so that it now
255        corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm).
256    o pkg/exf:
257      - allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some
258        calculations); change FWD experiment global_ocean.cs32x15
259        (#define ALLOW_ZENITHANGLE) to test/check that this code compiles.
260    o pkg/exf:
261      - In preparation for addition to NAMELIST, rename internal (_RL) parameter
262         {FIELD}startdate to {FIELD}StartTime
263        Note: new name also fit better the content, i.e, a start time in second.
264    o eesupp/src:
265      - add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF
266    o pkg/exf:
267      - add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters)
268        to allow to read-in Sensible & Latent Heat flux ;
269      - simplify pkg/exf main options:
270        1) move small piece of code (case ALLOW_ATM_TEMP undef) out of
271           exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is
272           compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined;
273        2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option
274           ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ;
275        3) improve options documentation in EXF_OPTIONS.h.
276    o pkg/ecco:
277      - cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and
278        ecco_summary.F: add passive tracer cost functions to gencost;
279        m_ptracer and m_boxmean_ptracer
280    o pkg/ctrl:
281      - ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input
282        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list
283        of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw,
284        xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn
285    o model/src:
286      - forward_step.F: pass myIter and myTime to ctrl_map_forcing as input
287        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing
288    o pkg/exf:
289      - exf_getffields.F: add to list of implemented gentim2d contol parameters:
290        xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask
291    
292    checkpoint66c (2017/01/19)
293    o verification:
294      - add new option "-src" to testreport to only produce source code (*.f),
295        including taf output src code (if using '-adm'/'-tlm' option).
296    o pkg/exf:
297      - add saltflx :: Net upward salt flux in psu.kg/m^2/s
298    o pkg/diagnostics:
299      - add run-time variable diagMdsDir to specify a subdirectory for
300        diagnostic output when mds is being used and mdsioLocalDir is not.
301    o pkg/mnc:
302      - mnc_utils.F: edit stop message
303    o pkg/autodiff:
304      - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER,
305        add HAVE_SYSTEM bracket around system call to mkdir
306    o pkg/profiles:
307      - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F,
308        profiles_readparms.F: call ALL_PROC_DIE before 'stop'
309      - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER,
310        add HAVE_SYSTEM bracket around system call to mkdir
311    o pkg/smooth:
312      - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop'
313      - smooth_init2d.F, smooth_init3d.F: move print statements to readparms
314      - smooth_readparms.F: add cleaner print statements from smooth_init?d.F
315    o pkg/exf:
316      - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
317        issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500
318        generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
319      - summary: skip detailed field report if not used (empty file-name).
320    o tools/xmakedepend:
321      - In case line editor "ed" is missing, switch to "sed" command to clean-up
322        Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
323    o pkg/exf:
324      - change definition of "hflux" input file to always include Short-Wave;
325        this is now consistent with hflux computation (if using bulk-formulae)
326        and hflux diagnostic & documentation (in EXF_FIELDS.h).
327    
328    checkpoint66b (2016/12/01)
329    o model & momentum pkgs:
330      - implement fully implicit bottom friction combined with implicit surf.
331        pressure, for now, only in hydrostic formulation:
332        + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
333          and run with selectImplicitDrag=2 ;
334        + currently missing diagnostics of bottom drag and vert. viscosity tendency;
335      - partial implicit time-stepping (bot. friction + vert. visc first, then
336        surf. press) corresponding to selectImplicitDrag=1 should be applicable
337        to NH formulation but not available until we solve for surf. pressure
338        increment (instead of full etaN).
339      - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
340        with implicit vertical viscosity.
341    o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
342      - this is a first version that includes many regularisations that may
343        not all be necessary, to be sorted out,
344      - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
345      - change one verification experiment in seaice_itd to use and test new code
346      - seaice_growth: catch a case where the argument of log can be zero
347        or smaller (important for code stability)
348    o model/src:
349      - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F
350        & solve_pentadiagonal.F to enable to re-used inverse matrix for solving
351        similar A.X'=Y' system (with same matrix A) in subsequent calls;
352        switch based on errCode (In/Out) argument value; in calling routines,
353        initialise errCode before first call.
354    
355    checkpoint66a (2016/10/18)
356    o pkg/bling:
357      - BLING package now loads in atmospheric pCO2 file using exf package routines
358        Enable with #define USE_EXFCO2 in BLING_OPTIONS.h
359    o model/src & pkg/ptracers:
360      - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R &
361        GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and
362        implicitDiffusion (respectively) are used (even without momImplVertAdv
363        or temp,salt,PTRACERS_ImplVertAdv).
364    o model/src & generic_advdiff:
365      - add parenthesis in main diagonal calculation of implicit vertical
366        diffusion matrix (impldiff.F & gad_implicit_r.F).
367        This affects results at machine truncation level; update output of many
368        verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
369    o pkg/mom_commom & generic_advdiff:
370      - add deep atmosphere and anelastic scaling factor in implicit vertical
371        advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
372    o model/src:
373      - remove few unnecessary temp array copies in solve_tridiagonal.F
374        & solve_pentadiagonal.F
375    
376    checkpoint65z (2016/09/28)
377    o pkg/seaice: fix multithreading for seaice_fgmres.F
378      - remove unecessary variables from common blocks
379      - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
380        basis, that are stored in commom blocks (including integer variable i1)
381      - clean up code a little by removing commented lines that refer to
382        original code
383      - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
384    o MITgcm manual:
385      - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
386        preliminary documentation for generic controls (8.3; ctrl.tex),
387        a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
388        ecco_costfunction.tex
389    o pkg/ecco:
390      - update and cleanup list of CCP options
391      - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
392        is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
393      - add checks that retired run-time options are not used, and in relation
394        to gencost_mask and gencost_errfile
395      - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
396        gencost_nrecperiod
397      - fix m_eta computation for virtual salt flux case
398      - add m_horflux_vol case (selected via gencost_barfile) that computes
399        transports via cost_gencost_boxmean (gencost_flag=-3)
400      - use gencost_flag more systematically (i.e., avoid using gencost_name)
401        for code switches (aside from physical variable selection)
402    o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
403      attempt appears to be a bit of a hack and my need some repair down the road
404    o pkg/exf:
405      - interpolation near South Pole: fix criteria on input field latitude.
406    o pkg/icefront & pkg/exf:
407      - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
408        from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
409    o pkg/exf:
410      - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
411        "exf_output_interp" (in namelist: EXF_NML_04); change output file name
412        (add suffix "_out" instead of a prefix); keep same record number as in
413        input file but always write record 1 first (to avoid a STOP in I/O S/R).
414        Change output file content by writing interpolated field before applying
415        land-sea mask (helpful for debug).
416      - 2 compon. vector interpolation with rotation: apply scaling factor on
417        each compon. (Eastward and Northward) just before rotation.
418    o pkg/bling:
419      - Cleaned package. Removed not needed code and comments.
420      - adjoint example now works
421        (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
422    o pkg/ptracers:
423      - add Bruno Deremble's code to complete the linear surface correction
424        for tracer conservation;
425      - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
426    
427    checkpoint65y (2016/07/29)
428    o pkg/debug (stats):
429      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
430        proc/thread mapping);
431      - fix Min & Max for case where 1 thread has only empty tiles;
432      - use RL variable to count number of wet grid points (with big domain,
433        can be too large to fit into integer*4).
434    o pkg/monitor:
435      - use RL variable to count number of wet grid points (but used only for del2)
436      - add new routine to compute Advective CFL within tracer time-stepping with
437        writing delayed until next monitor output.
438    o pkg/obcs:
439      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
440    o pkg/cal:
441      - calandar-dump: treat case myTime < timePhase in the same way as in
442        eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
443    o pkg/dic & seaice:
444      - fix compilation of ocean component for coupled atm+ocn model with
445        seaice dynamics & dic.
446    
447    checkpoint65x (2016/06/11)
448    o add a license text file in main MITgcm tree.
449    o added pkg/bling:
450      - intermediate complexity biogeochemical model
451      - see bling_description.txt for details
452      - verification experiment is global_oce_biogeo_bling (for now, in
453        Contrib/verification_other/); tested daily on baudelaire with gfortran.
454      - add entry point in pkg/gchem for new pkg "bling".
455    o pkg/seaice: fix tensile stength computation
456      - replace global field tensileStrength by tensileStrFac
457      - tensileStrFac can be computed once in S/R seaice_init_varia
458      - fortunately that does not affect any verification results
459    
460    checkpoint65w (2016/05/12)
461    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
462         with ECCO_CTRL_DEPRECATED defined
463    o verification/global_ocean.cs32x15:
464      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
465        with "selectNHfreeSurf=1".
466    o model/src (non-hydrostatic free-surface):
467      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
468        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
469      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
470        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
471        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
472        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
473      - Update output (changes at machine truncation level) of verification exp:
474        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
475        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
476    o pkg/seaice: ITD code
477      - fix picking up from a single category model by initialising
478        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
479      - split a long warning message in seaice_check_pickup.F into two lines,
480        because NEC SX-ACE cannot deal with the long line.
481    o model/src:
482      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
483    o pkg/seaice:
484      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
485    o pkg/seaice:
486      - add basal stress as parameterisation for grounding ice
487        following Lemieux et al. (2015)
488      - turn on by setting new parameter SEAICEbasalDragK2 to a value
489        larger than 0. Lemieux et al. (2015) recommend 15.
490      - The adjoint complains with extra recomputations so there is also a
491        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
492        order to postpone the problem
493      - compile the new code in lab_sea
494    o verification/halfpipe_streamice:
495      - update both TAF and OpenAD adm output (machine truncation differences)
496    
497    checkpoint65v (2016/04/08)
498    o verification/advect_xz:
499      - increase overlap size from 3 to 4 and add new secondary test for PQM
500        advection scheme (with mono & wino limiter).
501      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
502    o model/src:
503      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
504        added phi0Ref) to set vertical axis origin and phiRef origin;
505        keep Ro_SeaLevel for backward compatibility (with a warning).
506       According to coordinate and fluid type:
507        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
508        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
509        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
510        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
511      - remove Ro_SeaLevel from ATM experiment parameter files;
512      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
513        complement; update output.txt (changes at machine truncation level).
514    o pkg/seaice/seaice_evp.F
515      - simplify computation of deltaZ and zetaZ to simple averaging following
516        Bouillon et al. (2013). This removes a lot of code, but also changes
517        verification experiment lab_sea.hb87 -> updated
518    
519    checkpoint65u (2016/03/14)
520    o pkg/generic_advdiff:
521      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
522        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
523        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
524        testing and not for actual use.
525    o model/src:
526      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
527        origin r = rF(1);
528      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
529        in EOS for height coordinate: enable to include NH Pressure or to use
530        more accurate pressure vertical profile; options not linked to EOS type
531        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
532      - start to implement variable gravity (along vertical): for now, only with
533        z-coords (not even z*).
534      - add Ideal Gas equation of state for height coordinate.
535      - update OpenAD output (affected at machine truncation level) of exp:
536        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
537    o pkg/exf:
538      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
539        of exf interpolation (before any rescaling, rotation or interpolation
540        to velocity point) for each field that gets loaded from file. This option
541        identically mimics the input file organization (e.g. record numbers in year
542        by year input files) besides the change in horizontal grid.
543      - add rotateStressOnAgrid run-time switch so that wind stress fields
544        can be provided on the A-grid in zonal/meridional direction and
545        rotated on the fly. This only applies to the case when the exf
546        interpolation is off and rotateStressOnAgrid is false by default.
547    o model/src:
548      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
549        it's also used with pkg/atm_phys) and add few more parameters (but still
550        inactive, src code yet to come)
551    
552    checkpoint65t (2016/02/10)
553    o pkg/atm_phys:
554      - from Ruth Geen: add optical depth dependence on CO2 concentration.
555    o model/src:
556      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
557        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
558        Update output of exp. deep_anelastic (changes at truncation level).
559    o tools:
560      - add a hack in "remove_comments_sed" (used only with TAF) for recent
561        version of OpenMPI (shipped with FC.23): comment out the new header
562        file "mpif-sizeof.h" which causes problems to TAF.
563    o pkg/seaice:
564      - change the termination criterion so that maxits (SEAICElinearIterMax)
565        has an effect
566      - unify iteration parameters for implicit solvers (JFNK and Picard)
567        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
568        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
569        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
570        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
571        SEAICEnonLinTol     replaces JFNKgamma_nonlin
572      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
573      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
574        use with SEAICEuseKrylov
575    o pkg/seaice/seaice_lsr.F
576        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
577        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
578        an effect.
579    o pkg/seaice: add two new parameters
580      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
581        parameter is not in any namelist)
582      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
583        a preconditioner for the non-linear Newton iteration of the JFNK
584        solver
585    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
586      affects some experiments at truncation level:
587      - global_ocean.cs32x15.icedyn (11 digits),
588      - global_ocean.cs32x15.seaice (11 digits),
589      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
590      - also update global_ocean.cs32x15 adjoint and tangent-linear results
591    o pkg/salt_plume & pkg/thsice:
592      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
593        connect salt_plume flux to ATM-OCN coupling pkgs interface:
594       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
595         export to coupler interface) even without compiling pkg/salt_plume ;
596       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
597         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
598    o pkg/dic:
599      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
600        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
601        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
602      - move also update with values from ATM-OCN Coupler in the same new S/R
603        (previously done in ocn_apply_import.F).
604    o tools/adjoint_options:
605      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
606        has been changed on Jan 14, 2016.
607    o pkg/ggl90:
608      - add alternative discretisation of vertical shear (off by default), to
609        compute the mean (@ grid-cell center) of vertical shear compon instead of
610        vertical shear of mean flow (@ grid-cell center).
611      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
612        results on adjacent faces of cubed-sphere grids; this fix the restart.
613    o pkg/atm_compon_interf:
614      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
615        pass last value, stored directly before export to CPL ;
616        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
617      - remove atmSLPr from pickup files (no longer needed for restart)
618    
619    checkpoint65s (2016/01/13)
620    o eesupp & genmake2:
621       - first check for Function ETIME and, if it fails, then check for subroutine
622         ETIME and consistent output; use the appropriate version in timers.F
623    o model/src:
624      - to check restart test, add option to apply EXCH to U,V earlier, just before
625        integr_continuity; turned off by default.
626    o pkg/dic:
627      - remove CPP option USE_ATMOSCO2 (not needed)
628    o tools/tst_2+2:
629      - try to ignore difference between +0 and -0 in binary file, causing test
630        to fail for no good reason.
631    o eesupp & genmake2:
632      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
633        but also check (in genmake2) that test runs and returns meaningful results.
634    o coupler pkgs:
635      Finish implementation of optionally-exchanged variable switches (started on
636       Nov 12) with addition of few more exchanged fields, including 2-way exchange
637       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
638       advection in OCN component; this requires sequential coupling.
639      coupler (pkg/atm_ocn_coupler):
640      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
641        routines (useful for debug).
642      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
643         flux, DIC fields) if corresponding switch is ON.
644      - add option to export RunOff to OCN (to use for DIC river input)
645      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
646      components (pkg/atm_ & ocn_compon_interf):
647      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
648        optionally exchanged fields; add a check & stop in cpl_readparms.F.
649        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
650        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
651      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
652        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
653      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
654      - hold in common block coupler optionally-exchanged variable switch
655        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
656      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
657        this is intended to replace the OCN cplFldtave.* output files (not updated
658        to contain new additional exchanged fields).
659    o pkg/dic:
660      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
661    o pkg/thsice:
662      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
663        and writing of thsice pickup files.
664    o pkg/atm_compon_interf:
665      - move all field individual export-call out of cpl_export_import_data.F
666        into new S/R ATM_EXPORT_FIELDS
667    o pkg/atm_compon_interf:
668      - store state variables (for now, only thSIce fields) just before beeing
669        exported (in cpl_export_import_data.F, like on ocean side) instead of from
670        atm_store_my_data.F like all exported fluxes.
671      - new version of pickup_cpl: write field names into meta file and read meta
672        file to find field postion in pickup. Also only write/read fields meeded for
673        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
674    o pkg/dic:
675      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
676    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
677        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
678        value can be from domain [0,1] to average between the two methods
679    o pkg/atm_phys:
680      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
681        hold fixed in time).
682    
683    checkpoint65r (2015/12/21)
684    o pkg/seaice:
685        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
686        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
687    o pkg/seaice:
688      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
689        when SEAICEscaleSurfStress=.TRUE.,
690      - apply areaW and areaS in S/R seaice_calc_lhs
691    o pkg/atm_phys:
692      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
693        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
694        for individual contribution (convection, LSC cond, radiation)
695      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
696        information); activated with: solar_exponent=0. and wv_exponent=-1.
697    o pkg/ggl90:
698      - within IDEMIX add upper limit for horizontal group velocity to
699        avoid instability problems in the explicit horizontal diffusion term for
700        long time steps or high resolution
701    o pkg/diagnostics:
702      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
703        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
704    o testreport:
705      - remove "-v" (verbose option) in default mpirun command.
706    o pkg/seaice/seaice_growth:
707      - catch potential division by zero in ITD code, does not change
708        verification results
709    o pkg/ecco:
710      - retire old codes to the Attic. The calls to retired functions are
711        left in a commented form in case they ever need to be re-activated.
712      - ecco_check.F: issue warning if any old CPP option is
713        defined that corresponds to retired codes -- then stop.
714    o pkg/atm_compon_interf:
715      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
716        coupler: use last time-step value instead of average over cplSendFrq_iter
717        time-step, similar to what is done for seaIceMass.
718        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
719    o eesupp & genmake2:
720      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
721        <= remove until a fix is found for some ifort version on ia32 machine.
722    o pkg/seaice/seaice_evp:
723      - refine residual computation
724    
725    checkpoint65q (2015/11/18)
726    o pkg/seaice/seaice_evp:
727      - fix residual computations so that they no longer affect the actual
728        simulation code
729      - fix seaice_readparams to be able to actually set new parameters
730        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
731    o model/src:
732      - fix wrong truncation (single prec) from "FLOAT" function in expressions
733        like: deltaT*FLOAT(myIter) when myIter is large:
734         a) replaced by DFLOAT (if not seen by TAF);
735         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
736    o pkg/aim_v23:
737      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
738        when pickupSuff is set ; do write rolling pickups + at the end of the run.
739    o pkg/atm_ocn_coupler + ocn_compon_interf:
740      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
741        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
742        add corresponding call in DO_OCEANIC_PHYS.
743    o coupler pkgs:
744      Start a new way to set-up optionally-exchanged variables (previously, only
745       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
746       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
747       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
748       compononent param default can be set accordingly).
749      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
750       but rather applies to a group a fields (going both ways like for DIC)
751       and corresponds to an option of coupling config.
752      coupler (pkg/atm_ocn_coupler):
753      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
754        and read namelist directly (without eessup S/R calls) instead of
755        in the very un-flexible old way, 1 param per line, in fixed order;
756      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
757        cleanly in CPL_CHECK_CPLCONFIG
758      - add new coupling-exchange selectors (some not yet active) including
759        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
760                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
761      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
762        component ; called directly from coupler.F, after comp. registrations;
763      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
764         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
765          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
766      components (pkg/atm_ & ocn_compon_interf):
767      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
768        CPP header file in all pkg source files.
769      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
770        ATM/OCN_CHECK_CPLCONFIG;
771      - add error-counter to track errors (e.g., in "data.cpl") and to stop
772        cleanly in ATM/OCN_CHECK_CPLCONFIG;
773      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
774        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
775        before PACKAGES_READPARMS;
776      verification/cpl_aim+ocn/:
777      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
778        "data.cpl" for coupler (in input_cpl).
779    o eesupp/inc:
780      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
781        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
782        to always cumulate tile local-sum in the same order (still uses
783        MPI_Allreduce like standard code).
784      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
785        that are now identical to standard version (in eesupp/inc).
786    o pkg/shelfice:
787      - add SHELFICETransCoeffTFile for initializing spatially varying
788        heat and salt transfer coefficients
789    o pkg/atm_compon_interf & ocn_compon_interf:
790      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
791        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
792      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
793    o pkg/atm_ocn_coupler:
794      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
795    o pkg/rbcs:
796      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
797        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
798      - add a short report (to STDOUT) about RBCS-mask settings.
799    
800    checkpoint65p (2015/10/23)
801    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
802        there is no adjoint test for EVP, we don't know what it does to the adjoint
803        solution, but at least there are no more recomputation warnings left
804    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
805        a chance of giving the same results as a fully converged VP (JFNK) solver
806    o tools/adjoint_options/adjoint_diva:
807      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
808    o pkg/streamice:
809      - spotted bug in streamice_driving_stress using dyG where should have been dxG
810    o pkg/exf:
811      - remove STOP statement that prevented to use wind or (wind-)stress
812        interpolation for constant-in-time forcing fields (wind/stress period = 0).
813    o pkg/seaice:
814      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
815        5 additionals 2D fields and 6 new store directives
816      - change logic in seaice_readparms.F: EVP code can now be turned on in
817        various ways, setting SEAICE_deltaTev is no longer required,
818        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
819        or SEAICEaEVPcoeff
820    o pkg/shelfice/shelfice_thermodynamics.F
821      - redefining uLoc/vLoc to u/v, instead of 2u/v
822    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
823      - this is an intermediate state of a truely converging EVP that has
824        the potential of outperforming implicit VP methods, I do not recommend
825        using it yet.
826      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
827        and all parameters are hardwired
828      - for convergence it still requires very smooth regularisations, that means,
829        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
830        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
831        specific averaging appears to be required, still subject to tuning
832      - still needs cleaning and I need to turn parameter into runtime parameters
833      - add code to compute and print residuals of iteration, compile with
834        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
835    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
836      that entered with r1.54 on Sep04, 2015, -> update results
837    
838    checkpoint65o (2015/09/14)
839    o pkg/mom_vecinv & mom_common:
840      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
841        called from there.
842      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
843        allows to use Vector-Invariant form in deep atmos and anelastic formulation
844    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
845      and Koenig-Beatty+Holland (2012)
846      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
847      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
848      - requires an extra input argument for S/R seaice_calc_viscosities
849      - tensileStrength's depth dependence is different from Itkin et al. (2015)
850        (to be changed and played with, for now exponential)
851    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
852      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
853        by AREA according to Connelly et al. (2004), JPO.
854      - For EVP and the LSR solver, the implicit part of the drag term is
855        the only non-zero term in the denominator when there is no ice (which
856        prevented running the model with zero ice-ocean drag). If
857        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
858        (or zero main diagonals BU/BV) which need to be caught. A practical
859        consequence is that for open water, the momentum equation reduce
860        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
861        they happen to be zero, often leading to a non-zero solution over
862        open water.
863    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
864        efficient EVP method.
865      - introduce area-weighted averages for e12 (analogously to
866        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
867        remain, but also changing the order of terms in the previous average
868        changed the results as much) -> update experiment
869      - add SEAICE_DELTA_SMOOTHREG code
870      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
871        TEM-code
872      - adjust loop bounds so that only required fields are computed
873      - add new averaging code for zetaZ/deltaZ (again similar to
874        seaice_calc_viscosities.F), inactive by default for now (will change
875        results again), but will replace old code eventually
876    o eesupp/src:
877      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
878        to always cumulate tile local-sum in the same order
879        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
880        Still uses MPI_Allreduce (like standard code) but on array of tiles
881        and should be faster than GLOBAL_SUM_SEND_RECV code.
882      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
883        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
884      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
885         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
886         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
887         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
888         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
889    
890    checkpoint65n (2015/07/29)
891    o pkg/thsice:
892      - add a warning when used with pkg/aim but without updating SST
893        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
894    o pkg/offline:
895      - change where Offline-Fields are loaded, from load_fields_driver.F to
896        directly within FORWARD_STEP, just after updating iter number and time;
897      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
898        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
899       These changes allow:
900        a) to recover exactly on-line results using deltaToffline=deltaTClock,
901        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
902        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
903        time-step, both with GM & KPP files and with recomputing these fields;
904        b) no needs to switch on staggerTimeStep anymore;
905        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
906      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
907    o pkg/offline:
908      - change (rarely used) offset-iteration parameter to an offset time (in s):
909        can easily recover previous offset-iter effect by setting offset-time
910        (offlineTimeOffset) to offset-iter x deltaToffline;
911      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
912        in KPP as part of surface buoyancy forcing) in offline run.
913      - fix ptracers KPP non-local term in the case where KPP is re-computed.
914    o OpenAD
915      - Adding preliminary ggl90 test to OpenAD verification.
916        Config. with ggl90 currently diverges after 64 time steps
917        so will need more work to become more stable
918      - Adding preliminary kpp test to OpenAD verification.
919        required small tweakes in kpp_routines.F
920      - Merge and update from Krishna Narayanan's contrib area:
921        * Add one variable for preliminary OpenAD DIVA
922        * Add replacement time-stepping for OpenAD DIVA
923        * genmake2 flag -diva (but only for OpenAD; preliminary)
924        * required modifs for OAD_support
925        successful preliminary test for tutorial_global_oce_biogeo/
926    o pkg/seaice:
927      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
928      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
929        delta with a smooth function in s/r seaice_calc_viscosity
930        (no effect on EVP)
931      - rename local suffix "sqr" into "sq" for more consistent variable names
932    o pkg/seaice:
933        add new parameter SEAICE_deltaMin that is used ***only***
934        for regularizing Delta (and nothing else, like the parameter
935        which is also used for all sorts of things SEAICE_EPS).
936        Defaults to SEAICE_EPS for backward compatibility only.
937    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
938        the wrong key by inialising it before use -> fixes a recomputation
939        problem but does not fix the gradient
940    o pkg/layers:
941      - move resetting of flux arrays to outside the iLa loop
942        (this caused layers_diapycnal to not work with more than one layer coord.)
943      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
944    o pkg/layers:
945      - remove from common block 3D layers fields (used to diagnose transport
946        in tracer coords) and declare them as local arrays in layers_calc.F
947    o pkg/seaice:
948      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
949        in lab_sea forward experiment (changes results -> updated)
950      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
951    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
952       computations; for SEAICE_VECTORIZE_LSR
953      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
954        sweep to the outside,
955      - remove store directives and add "CADJ loop sequential" directives
956        in analogy to model/src/solve_tridiagonal.F
957      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
958        boundaries to yield more readable code. This has also the charming side
959        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
960        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
961        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
962        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
963        an additional option)
964       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
965       but the adjoint gradients (which are affected by this change) still explode.
966    o coupler (atm & ocn _compon_interf):
967      - avoid using Exch2 IO mapping if not suitable.
968    
969    checkpoint65m (2015/06/15)
970    o pkg/layers:
971      - clean-up old parameters setting (from Sep 2012):
972        + remove old parameters setting from common block (declared locally);
973        + stop if any old parameter is mixed with new parameters;
974        + check for valid or consistent parameter setting (e.g., layers_name)
975      - check that layers_bounds for Pot.Density are in the right range;
976        this is supposed to catch un-updated setting after recently shifting
977        potential density field "prho" by -1000 (now in "sigma" scale).
978    o pkg/layers:
979      - Added missing call to layers_fill for keeping track of tottend in
980        pkg/diagnostics/diagnostics_fill_state.F
981    o pkg/layers:
982      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
983        of diapycnal fluxes
984    o pkg/layers:
985      - reverted changes to interpolation to previous treatment; there
986        was never actually a problem
987    o pkg/layers:
988      - fix interpolation of layers tracers in the presence of partial cells
989      - add lots of new functionality to compute water mass transformation
990        (enabled by CPP flag LAYERS_THERMODYNAMICS)
991      - add new calls from main code (diags_oceanic_surf_flux.F,
992        thermodynamics.F, impldiff.F) and gad to save the necessary fields
993        for layers_thermodynamics calculations
994    o pkg/ptracers:
995      - add capability of stepping a passive tracer forward without advection
996        by setting PTRACERS_advScheme to 0.
997    o pkg/diagnostics:
998      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
999    o pkg/layers:
1000      - shift potential density field "prho" by -1000 for density layer averaging so
1001        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
1002        Note that density bin boundaries (layers_bounds in data.layers) have
1003        to be set accordingly (i.e., shifted, in sigma scale).
1004    o pkg/layers:
1005      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
1006      - fix calculation of layer non-weighted velocity and layer probability
1007      - add diagnostics for pot.density used for layer averaging
1008    o pkg/seaice:
1009      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
1010        positiveness, modify a few comments and improve variable names,
1011      - the changed computation of deltaC affects most seaice-related
1012        experiments at the truncation level.
1013        seaice_itd.thermo is affected by far the most, with
1014        only 7 digits of agreement remaining; update experiments.
1015    
1016    checkpoint65l (2015/05/04)
1017    o pkg/shelfice:
1018      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
1019        factor drKp1 to zero where it is negative (ie. do not use
1020        SHELFICEBoundaryLayer if hFacC>1)
1021      - the same for factor drLoc in shelfice_forcing.F
1022    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
1023        with modules in ptracers, when using testreport option "-small_f"
1024    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
1025      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
1026    o verification/testreport
1027      - add new option -small_f
1028        with this option testreport first makes the target small_f (*.f files)
1029        before running make (all). This is useful for explicit inlining when
1030        all sources need to be full available.
1031    o pkg/exf/exf_interp.F:
1032        remove previous changes related to reverse (decreasing) input grids latitude
1033    
1034    checkpoint65k (2015/04/01)
1035    o pkg/ecco:
1036        fix missing cosphi initialization; use eccoiter in place of optimcycle;
1037        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
1038        instead of active read/write
1039    o pkg/ctrl:
1040        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
1041        instead of active read/write.
1042    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
1043        return if .NOT.useAUTODIFF
1044    o pkg/seaice: add CPP brackets (cost function related).
1045    o model/src:
1046        add useAUTODIFF run time switch.
1047    o pkg/exf/exf_interp.F:
1048        add code to allow input grids with latitude starting in the north (i.e. when
1049        j=1 corresponds to northern edge of field); modify global_with_exf to test
1050        this feature.
1051    o verification/testreport:
1052      - replace "grep -A3" with POSIX conformal sed command, because there are
1053        implementations of grep that cannot do contextual searches
1054      - replace "cat -n" by "nl" (two occurrences), because not all implementations
1055        of "cat" have the option "-n"
1056    o model/src:
1057        add new file gsw_teos10.F that contains 3 functions, more or less a copy
1058        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
1059        convert from conservative to potential temperature. For now they are not
1060        called anywhere.
1061    o pkg/ggl90: make "useIDEMIX" useful
1062      - re-organize code in s/r ggl90_calc a little to move computations that
1063        are different for idemix into separate loops (changes verification
1064        experiment idemix at truncation level, 12 digits remain -> updated)
1065      - requires 2 new 2D fields KappaM, verticalShear
1066      - make hFacI and recip_hFacI local 3D variables that are passed to
1067        s/r ggl90_idemix
1068      - fix and improve some comments
1069    
1070    checkpoint65j (2015/02/25)
1071    o pkg/openad
1072      - synchronize seawater.F with version in model/src: replace routine
1073        body of sw_temp by calling sw_ptmp and fix/add a few comments.
1074    o pkg/mnc:
1075      - change default value of pickup_read/write_mnc params to FALSE
1076        (since few features are missing in reading MNC pickup files).
1077    o model/src:
1078      - change default (background) vertical diffusivity for salt to be the
1079        temperature (background) vertical diffusivity.
1080      - change background vertical diffusivity in vertical mixing pkgs ggl90,
1081        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
1082        This makes ptracers default diffusivity (that uses salt diffKr) more
1083        consistent with vertical mixing schemes.
1084    o verification/testreport:
1085      - fix typo in "-pcls" option ;
1086      - put temp files in /tmp (instead of in local dir)
1087      - add option "-ncad" to use genmake2 new option "-nocat4ad"
1088      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
1089    o pkg/ggl90 (idemix code):
1090      - apply few fixes ; add some missing "_d 0" ; update output of exp.
1091        global_ocean.90x40x15.idemix
1092    o OpenAD
1093      - enable active file I/O and begin removal of work-around code
1094        for OpenAD for handling control variables (memory vs. active files)
1095      - new CPP options file OPENAD_OPTIONS.h
1096      - revert to genarr2d gradient check for hs94.1x64x5
1097      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
1098      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
1099    o tools/genmake2:
1100      - add option for an alternative Makefile (from Martin) where multiple
1101        source files are sent to TAF (instead of all in one file).
1102    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
1103      - code provided by Carsten Eden as an extension of ggl90
1104      - so far the code is turned on within ggl90 by setting a CPP-flag at
1105        compile time; a runtime flag implementation is not yet complete
1106      - tested in new verification experiment global_ocean.90x40x15.idemix
1107    o verification:
1108      - reduce length of the AD test run by half for experiments
1109        global_ocean.cs32x15 (std + thsice) and isomip
1110      - enable active file I/O for OpenAD, adjust verifications accordingly
1111      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
1112    o verification/testreport:
1113      - fix two non-POSIX sed statements so that there are no error messages
1114        on Mac OS X
1115      - replace hostname -s with hostname | sed 's/\..*$//'
1116    o model/src/seawater.F:
1117      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
1118        (following the matlab code), which would have avoided the bug caught
1119        by Matt (see below) in the first place
1120    o pkg/shelfice:
1121      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
1122        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
1123      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
1124        ice-shelf case (i.e., within surface level).
1125      - add config summary in shelfice_check.F
1126      - remove global variable recip_SHELFICElatentHeat and replace by a local
1127        variable recip_latentHeat
1128      - introduce diagnostics for friction velocity uStar (in case of
1129        SHELFICEuseGammaFrict)
1130      - change verification experiment isomip.htd:
1131        + start from pickup (as input_ad at nIter0=8640)
1132        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
1133        + test SHELFICEuseGammaFrict = .TRUE.
1134        + test SHELFICEadvDiffHeatFlux = .TRUE.
1135    o model/src:
1136      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
1137        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
1138        update output of experiments global_with_exf.yearly and isomip (all 6).
1139    o pkg/shelfice:
1140      - change setting of kTopC to also be zero where there is no ice-shelf.
1141      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
1142        ice-shelf is.
1143      - first attempt to get RealFreshWaterFlux effects: for now, only without
1144        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
1145    o pkg/seaice: add the option to prescribe a fixed thickness PDF
1146      for thermodynamic calculations
1147      - because of divisions of the type 7/7 not exactly equal to 1, this change
1148        affects results of some verification experiments by up to 4 digits:
1149        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
1150        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
1151        adjoint: lab_sea, lab_sea.noseaicedyn
1152        -> updated
1153    
1154    checkpoint65i (2015/01/23)
1155    o model/src:
1156      - change units of frictionHeating field from W to W/m^2
1157      - fix bug in frictional heating from stratospheric drag in
1158        S/R ATM_PHYS_TENDENCY_APPLY_V
1159      - with synchronous time-stepping: move resetting to zero of frictionHeating
1160        field from load_fields_driver.F to thermodynamics.F ;
1161      - add diagnostics for frictional heating.
1162    o model/src & gmredi K3D:
1163      - add frictionHeating field to pickup-files (for synchronous time-stepping)
1164      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
1165      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
1166        and name in pickup file).
1167      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
1168    o model/src:
1169      - move (from ini_forcing.F) initialisation of all arrays in header file
1170        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
1171        (since Nov 2012) with option selectAddFluid=1.
1172    o pkg/shelfice:
1173      - change units (+ document) of newly added field "shelfIceMassDynTendency"
1174      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
1175    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
1176    o pkg/seaice: two new runtime parameters:
1177      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
1178        long overdue
1179      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
1180        parameterization of tensil stress for fast ice (does not do anything yet)
1181    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
1182        for LSR: move checking overlaps out of JFNK-if-block
1183    o pkg/atm_phys:
1184      - move copy of grid and dynamical fields out of atm_phys_driver.F into
1185        new S/R ATM_PHYS_DYN2PHYS.
1186      - fix level height for Linear Free-Surf case (to be consistent with
1187        fixed-in-time pressure levels).
1188    o pkg/mom_common (bottomdrag):
1189      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
1190        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
1191        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
1192    o pkg/shelfice (u/v_drag):
1193      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
1194      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
1195        (now similar to shelfice_u_drag.F)
1196      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
1197        from mom_vecinv.F (similar to mom_fluxform calls).
1198    o pkg/mom_common (bottomdrag):
1199      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
1200      - add options for alternative discretisation of velocity norm in quadratic
1201        bottom drag: averaging of grid-cell-center KE to U.point and V.point
1202        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
1203        improves when averaging only the other component (e.g. vVel for U bottom
1204        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
1205      - add options (bottomVisc_pCell) to account for partial-cell in bottom
1206        friction (no-slip BC) thus getting the true distance from the bottom;
1207        off by default since this also reduces model stability (explicit bottom
1208        friction). Changes produce different machine truncation with linear-drag
1209        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
1210        front_relax (bvp & mxl, 10 & 11 digits).
1211    o model/src & mom pkgs:
1212      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
1213        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
1214      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
1215        just copy level Nr value to level Nr+1.
1216    o doc:
1217      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
1218    o pkg/shelfice:
1219      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
1220        SHELFICE.h: move array shelficemass to init_varia, initialise
1221        from array shelficemassinit, which is set in init_fixed and
1222        has option to be set from file; introduce array
1223        shelficeMassDynTend array, set thru file in init_fixed
1224      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
1225        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
1226        pkg/streamice
1227      - shelfice_thermodynamics.F: call shelfice_step_icemass if
1228        SHELFICEMassStepping = .true.
1229      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
1230    
1231    checkpoint65h (2014/12/17)
1232    o verification/global_ocean.90x40x15, global_ocean_ebm:
1233      - update to generic controls.
1234    o pkg/ctrl:
1235      - ctrl_map_ini_genarr.F: test for igen>0
1236      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
1237      - move gentim2d part of ctrl_map_ini_genarr.F to
1238        new separate routine : ctrl_map_ini_gentim2d.F
1239      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
1240        add time variable weights and cyclic controls (time mean,
1241        seasonal cycle, etc) capabilities to gentim2d
1242    o pkg/ecco:
1243      - move reading of error, conversion to weights from
1244        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
1245    o global_oce_llc90, cs32:
1246      - activte sbo.
1247      - CTRL_SIZE.h : add maxCtrlProc.
1248      - activate the new genctrl capabilities.
1249      - update following reorganization of global_oce_input_fields.tar.gz  
1250    o pkg/ctrl/ctrl_ad_diff.list:
1251      - add missing ctrl_init_rec.f
1252    o tools/OAD_support/keepOriginal:
1253      - add ctrl_init_rec.F
1254    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
1255      - avoid recomputations of xx_gentim2d_dummy.
1256    o momentum diagnostics:
1257      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
1258        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
1259    o pkg/seaice/seaice_lsr.F:
1260      - fix computation of BU/BV, make sure they are non-zero, only necessary
1261        for cubed sphere exchanges and SEAICE_OLx/y>0.
1262        This makes calling s/r fill_cs_corner_rl obsolete (removed).
1263    o verification/global_ocean.cs32x15/input.seaice
1264      - add test for strong implicit coupling and restricted addtive Schwarz
1265        methods for LSR
1266      - update results/output.seaice.txt
1267    o verification/tutorial_global_oce_biogeo:
1268      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
1269        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
1270        update output_adm,_oadm,_tlm.txt
1271    o pkg/dic:
1272      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
1273      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
1274        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
1275    o verification/tutorial_global_oce_biogeo:
1276      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
1277        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
1278        update output_adm,_oadm,_tlm.txt
1279    o eesupp/src:
1280      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
1281        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
1282    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
1283      LSR (following Hutchings et al. 2004)
1284      - introduce zetaZ as a global variable (requires adjustments in
1285        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
1286        in seaice_calc_viscosities.F
1287      - new flag SEAICEuseStrImpCpl (default off)
1288      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
1289        momentum equations
1290      - JFNK-solver (preconditioner) adjusted to allow using this method
1291        (where it does not have any positive effect)
1292    o pkg/seaice
1293      - add overlap for restrictive additive Schwartz method also to LSR, but
1294        turn it off by default (because it only seems to work for non-cubed
1295        sphere/llc topologies)
1296    o pkg/autodiff
1297      - add extra exchanges in addummy_in_steppging also for mnc output
1298    o pkg/seaice:
1299      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
1300        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
1301    o pkg/obcs:
1302      - add option to specify domain-connected piece Id along OB though files
1303        (for now, only used to diagnose PhiVel; default =1 -> global correction)
1304      - modify obcs_diag_balance.F to process each connected-part separately;
1305        exclude OB where Id = 0 but keep the full divergence there (-> constant
1306        Psi along this portion of OB and all inflow derived from grad(Phi))
1307      - add example of OB-conect files in verification/so_box_biogeo/input.
1308    o pkg/diagnostics:
1309      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
1310      a) use non zero matrix element across OB and solve for Phi 1 grid point
1311         outside OB (i.e, where tracer OBCS are applied).
1312      b) global imbalance of inFlow/outFlow across OB: instead of modifying
1313         velocity across OB, spread it uniformly along the OB in the RHS.
1314    
1315    checkpoint65g (2014/11/19)
1316    o pkg/diagnostcis:
1317      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
1318    o pkg/my82,pp81,kl10:
1319      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
1320        field diffKr as background diffusivity to set minimum diffusivity value.
1321    o pkg/seaice:
1322      - add new parameter SEAICEuseEVPrev (for revisited EVP by
1323        Bouillon et al 2013)
1324      - add SEAICE_evpAlpha/Beta to namelist
1325      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
1326        involve trivial re-ordering of divisions/multiplications that should not
1327        have any effects, but ... they do change the results of lab_sea.hb87 so
1328        that only 2 digits of agreement remain, in line with the general
1329        instability/fragility of the evp-code. For now, I do not care and just
1330        update the verification experiment
1331    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
1332      - remove xx_genarr2d_numsmooth etc
1333      - use xx_genarr2d_preproc etc instead
1334      - carry out smooth_correl2D at initialization stage rather than during
1335        time stepping.
1336      - get smoothOpNb from xx_gentim2d_preproc
1337    o global_oce_cs32 :
1338      - add test of generic ecco capabilities.
1339    o pkg/exf/exf_getsurfacefluxes.F :
1340      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
1341    o pkg/ctrl,ecco :
1342      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
1343        is defined.
1344    o pkg/seaice: add diagnostics for Delta (deformation parameter)
1345    o model/src:
1346      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
1347        diffusivity (background) is specified but ignored.
1348    o verification:
1349      - in testreport, convert hostname to lower case for default output dir name
1350    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
1351    o pkg/dic: add modifications from Hajoon:
1352      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
1353      - light attenuation: add self-shading effect by climatological Chlorophyll
1354        (read from file).
1355    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
1356        compiles when SEAICE_ALLOW_DYNAMICS is undefined
1357    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
1358        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
1359        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
1360        approach where CPP_OPTIONS.h includes an omnipotent
1361        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
1362    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
1363        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
1364    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
1365        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
1366        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
1367    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
1368      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
1369      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
1370      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
1371      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
1372    o pkg/ctrl,ecco,exf :
1373      - remove variables associated with NON-generic costs,
1374        unless ECCO_CTRL_DEPRECATED is defined.
1375      - remove NON-generic NON-obcs controls,
1376        unless ECCO_CTRL_DEPRECATED is defined.
1377    o pkg/ctrl : added ctrl_local_params.h
1378    o pkg/ecco : added ecco_local_params.h
1379    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
1380        experiments, which will progressively be removed once the
1381        experiments are revised to use only generic controls/costs.
1382    
1383    checkpoint65f (2014/10/13)
1384    o pkg/ctrl, ecco, seaice : minor changes in headers
1385    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
1386        cost function and control capabilities added since checkpoint65c.
1387    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
1388    o pkg/ecco: increase modularity and improve logic
1389      - ecco_toolbox.F (new) : basic operations that are often used,
1390        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
1391        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
1392      - cost_gencal.F (new) : determine filnames and records.
1393      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
1394      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
1395        and exploit the above functions leading to more compact code.
1396      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
1397      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
1398        using_ers, using_gfo, using_mdt is now only defined within gencost)
1399    o pkg/ecco: extend generic cost capabilities
1400      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
1401        capabilities via gencost_preproc (+ _c,_i,_r related params),
1402        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
1403        gencost_outputlevel arguments to cost_generic
1404      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
1405        and active_read, making room for gencost_preproc to take effect.
1406        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
1407      - pkg/ecco/cost_generic.F :
1408        compute and store misfit maks*(model-data) in localdif that is
1409        then used in cost and for output, output misfit if outlev.GT.0
1410      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
1411        rather gencost_barfile for deciding whether to write barfile
1412      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
1413      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
1414        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
1415      - pkg/ecco/ecco_summary.F : report gencost variables
1416      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
1417    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
1418    o pkg/ecco: internal re-organization
1419      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
1420        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
1421        mv relevant variables definition from ecco_cost.h to ecco.h,
1422        make sure gencost routines only include ecco.h)
1423      - throughout : add missing CCP switches, rm unused variables,
1424        and rm un-necessary CPP switches
1425      - throughout gencost routines : replace modelstartdate with
1426        gencost_startdate when needed
1427      - cost_bp_read.F : use arguments, instead of common blocs
1428        so that it can be used also by (new) cost_gencost_bpv4.F
1429      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
1430      - ecco_phys.F : compute etanFull
1431      - ecco_readparms.F : rename using_topex as using_tpj, add
1432        bpv4-grace to gencost list, initialize added parameters
1433      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
1434    
1435    checkpoint65e (2014/09/28)
1436    o pkg/obcs:
1437      - replaced the just-added CPP options with run-time variables
1438        (see pkg/obcs/OBCS_PARAMS.h for details)
1439    o pkg/obcs:
1440      - add additional CPP options for sponge boundary layers
1441        (see pkg/obcs/OBCS_OPTIONS.h for details)
1442    o pkg/atm_phys:
1443      - implement simple (obliquity only, assuming circular planet orbit)
1444        seasonal cycle for incoming insolation ; used when run-time parameter
1445        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
1446    o pkg/exf, pkg/ecco, pkg/ctrl:
1447      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
1448      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
1449      - implement gentim2d for xx_tauu, xx_tauv
1450    o pkg/ctrl, pkg/ecco :
1451      - fix and complement the generic controls implementation
1452    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
1453        pkg/shelfice/shelfice_thermodynamics.F,
1454        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
1455        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
1456      - add weight in CTRL_GET_GEN calls
1457    o pkg/ctrl :
1458      - ctrl_get_gen.F : add weight as input parameter, and apply
1459        it directly rather than using smooth_correl2Dw (to be retired).
1460      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
1461    o pkg/ctrl :
1462      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
1463        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
1464      - re-activate ctrl_summary (call in ctrl_init.F)
1465    o pkg/ctrl/ctrl_cost_gen.F :
1466      - fix CCP brackets, remove un-necessary myiter, mytime
1467    o pkg/ecco, pkg/ctrl :
1468      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
1469      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
1470      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
1471      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
1472    
1473    checkpoint65d (2014/09/15)
1474    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
1475      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
1476        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
1477    o pkg/ctrl/ctrl_map_ini_genarr.F :
1478      - remove compilation failure
1479      - replace hard coded example
1480      - use ctrl_map_ini_gen2D, 3D
1481    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
1482      - on/off switch based upon xx_genarr2d_weight,3d
1483    o src/packages_init_variables.F :
1484      - regroup pkg/estimation calls
1485      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
1486        (moved to ctrl_init_variables)
1487    o cost/cost_init_varia.F :
1488      - remove ecco_cost_init_varia
1489        (moved to ecco_init_varia)
1490    o ctrl/ctrl_init_variables.F :
1491      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
1492      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
1493    o ctrl/ctrl_map_ini.F :
1494      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
1495        (moved to ctrl_init_variables)
1496    o ctrl/ctrl_map_ini_ecco.F :
1497      - remove ECCO_PHYS (mv to ecco_init_varia)
1498      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
1499    o ecco/ecco_ad_diff.list :
1500      - add ecco_init_varia.f
1501    o ecco/ecco_init_varia.F
1502      - new routine
1503    o pkg/streamice:
1504      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
1505        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
1506      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
1507    o pkg/generic_advdiff:
1508      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
1509    o pkg/exf:
1510      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
1511         xxg_precip capability
1512      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
1513    o pkg/ctrl:
1514      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
1515    o model/src/load_fields_driver.F :
1516      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
1517        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
1518    o OpenAD verification experiments:
1519      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
1520        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
1521        for now, only in pkgs used in OpenAD verification experiments.
1522      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
1523        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
1524        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
1525        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
1526    o OpenAD verification tests:
1527      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
1528      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
1529        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
1530      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
1531        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
1532    o model/src & generic_advdiff:
1533      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
1534        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
1535        dynamics requires valid tracer forcing only over tile interior but, for
1536        some diagnostics, may need to extend it over 1 point in tile halo region.
1537      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
1538        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
1539        setting in temp/salt/ptracer_integrate.F
1540    o pkg/dic:
1541      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
1542        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
1543        in gchem_forcing_sep.F
1544    o pkg/autodiff & obcs:
1545      - add storage of current OB values for U & V (was already done for T & S).
1546    
1547    checkpoint65c (2014/08/30)
1548    o pkg/dic:
1549      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
1550        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
1551        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
1552    o verification:
1553      - new experiment testing OBCS and DIC pkgs, using params & output from
1554        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
1555        passage: take OBCS from the last year of a 2 yrs simulation and initial
1556        conditions from t=1.yr while keeping the same forcing.
1557    o model/src:
1558      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
1559        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
1560    o pkg/diagnostics (Stats-Diags):
1561      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
1562        a) refine region where stats are computed, excluding where arrhFac=0 ;
1563        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
1564        c) extend regional stats over the region edges (for U or V pt location).
1565    o pkg/gchem:
1566      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
1567        pkg/dic is currently changing/updating ptracers values beyond the OB).
1568    o verification (hs94):
1569      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
1570        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
1571        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
1572        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
1573    o pkg/ptracers:
1574      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
1575        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
1576      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
1577        with AB-2 code (so that it get tested).
1578    o model/src:
1579      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
1580        with AB-2 code (previously only available with AB-3 code).
1581        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
1582        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
1583        there, by calling CYCLE_AB_TRACER).
1584    o pkg/generic_advdiff:
1585      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
1586        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
1587        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
1588        S/R temp/salt/ptracers_integrate.F
1589    o model/src & pkg/ptracers:
1590      - remove common block variables gT,gS (in DYNVARS.h), except when
1591         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
1592      - remove common block variable gPtr.
1593    o model/src & pkgs:
1594      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
1595         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
1596         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
1597         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
1598      + change accordingly all calling S/R.
1599      - use local temperature/salinity/ptracer tendency array (without bi,bj)
1600        in S/R temp/salt/ptracers_integrate.F
1601    o pkg/seaice:
1602      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
1603        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
1604      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
1605        in seaice_lsr
1606      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
1607        in s/r seaice_lsr_calc_coeffs
1608    o pkg/mdsio:
1609      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
1610        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
1611        too long (e.g., > MAX_LEN_FNAM/2 )
1612    
1613    checkpoint65b (2014/08/12)
1614    o pkg/matrix:
1615      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
1616    o model/src:
1617      - fix initialisation of geothermalFile; compile geothermal-flux code in
1618        natl_box verification experiment.
1619    o model/src & pkg/down_slope:
1620      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
1621      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
1622        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
1623        results at machine truncation level: update output of experiments
1624        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
1625    o pkg/diagnostics (Stats-Diags):
1626      - do not cumulate the full volume when DIAGNOSTICS_FILL is
1627        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
1628        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
1629        times (but Min,Max and StD are still wrong).
1630    o model/src:
1631      - add geothermal flux forcing: read in ini_forcing.F as time-constant
1632        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
1633    o model/src:
1634      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
1635        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
1636        arrays are already updated while adjustments (filters, conv.adjustment) are
1637        still applied later, in S/R TRACERS_CORRECTION_STEP.
1638    o model/src:
1639      - store in common bloc array "rhoInSitu" the virtual potential temperature
1640        anomaly that is used to compute geopotential: this make the atmos code
1641        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
1642    o pkg/seaice/seaice_lsr.F
1643      - rename integer variable ilcall to ipass (that's what it is called
1644        in the residual diagnostics
1645      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
1646        default) for improved non-linear convergence of the first few steps
1647      - adjust a few comments and add new ones to explain some of the store
1648        directives
1649    o pkg/generic_advdiff (& ptracers):
1650      - re-work the code to check for valid advection scheme and for minimum
1651        size of overlap (now stored in local common bloc in gad_advscheme.F)
1652    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
1653      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
1654      - add an auxilliary variable "bet" and fix store directives and keys in
1655        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
1656        less exact gradients in my tests); but there are still
1657        recomputation warning (although gradients are sort of OK), when
1658        SEAICE_LSR_VECTORIZE is not defined, so this flag and
1659        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
1660      - update verification experiments lab_sea.
1661      - change some comments in S/R seaice_calc_viscosities
1662    o model/src:
1663      - if staggerTimeStep=T, always apply exchange to velocity field in
1664        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
1665        (independent of using multi-dim advection or not); no effect on FWD run
1666        but affects AD results (at machine truncation level): update output of
1667        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
1668        and isomip (oad: 12.d).
1669    o pkg/generic_advdiff:
1670      - stop if doAB_onGtGs is set to FALSE but ignored
1671      - refine warning related to stability of tracer time-stepping
1672        regarding internal wave dynamics.
1673      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
1674        on staggerTimeStep & implicitIntGravWave (will now get a warning
1675        if potentially unstable).
1676    o pkg/kl10:
1677      - add new pkg "kl10" for mixing due to internal wave breaking, from
1678        http://www.sciencedirect.com/science/article/pii/S1463500310000144
1679        (contribution from Jody Klymak), tested in verification experiment
1680        verification/internal_wave/input.kl10/
1681    o isomip experiment:
1682      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
1683        (input.htd) and update the output.
1684    o cd_code experiments:
1685      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
1686        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
1687        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
1688        update the corresponding output.
1689    o pkg/seaice:
1690      - reduce the number of include files and store directives in
1691        S/R seaice_lsr_tridiagu/v
1692      - change the order of loops in one case in S/R seaice_lsr_tridiagv
1693        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
1694        get rid off one store directive (a TAF bug?)
1695      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
1696        S/R seaice_lsr_tridiagv to change the loop range for consistency
1697      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
1698      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
1699        S/R seaice_lsr_tridiagu/v (requires update of
1700        offline_exf_seaice/input.dyn_jfnk)
1701    
1702    checkpoint65a (2014/07/27)
1703    o model/src:
1704      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
1705        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
1706        (topo in p-coords, ice-shelf in z-coords); update output of experiments
1707        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
1708    o model/src:
1709      - collect momentum forcing tendency into local 2-D array (passed as argument
1710        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
1711        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
1712        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
1713      - collect T & S forcing tendency into local 2-D array (passed as argument to
1714        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
1715        affects results at machine truncation level (e.g., ocean: if using
1716        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
1717        correction due to vertical advection).
1718      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
1719        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
1720        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
1721        obcs_ctrl (ad & fwd grd @ 12 & 7).
1722    o pkg/ptracers & diagnostics:
1723      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
1724        title (to avoid some unexpected truncation); sort out ptracers diags units.
1725      - collect ptracer forcing tendency into local 2-D array (passed as argument
1726        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
1727    
1728    checkpoint65 (2014/07/18)
1729    o pkg/fizhi:
1730      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
1731        affects results at machine truncation level. Update output of experiments
1732        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
1733    o pkg/seaice: more clean up
1734      - rename TAF common block tapes to be more consistent and remove
1735        unnecessary duplicates
1736      - add store directives to remove more recomputations, but use smaller
1737        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
1738        The idea behind this flag is to reduce the memory footprint when the
1739        adjoint of the LSR is not required. As of now, defining the flag
1740        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
1741        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
1742        For experiment offline_exf_seaice, this means on a linux box with gfortran
1743        nearly a factor of 10 (but keep in mind there is mostly seaice code in
1744        this experiment):
1745        > size mitgcmuv_ad
1746        text    data        bss     dec        hex
1747        5100659 1216  220458952  225560827  d71c8fb
1748        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1749        but only a moderate increase of 36% for global_ocean.cs32x15:
1750        text    data        bss     dec        hex
1751        6695027 1648 1014578664 1021275339 3cdf6ccb
1752        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
1753      - note: there are still recomputations in global_ocean.cs32x15 and
1754        offline_exf_seaice and the gradient agreement changes (gets a
1755        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
1756      - in general, the AD gradients still are wrong
1757    o OpenAD
1758      - clean up code_oad/ directories somewhat by moving files
1759        dontCompile, dontTransform, keepOriginal to OAD_support/
1760    o model/src:
1761      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
1762        (not currently tested): add dissipation terms before NLFS rescaling of
1763        tendencies (previously done after).
1764    o pkg/diagnostics:
1765      - write stats-diags in ascii file with more digits (same as in monitor).
1766    o pkg/down_slope:
1767      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
1768        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
1769    o model/src:
1770      - new file "apply_forcing.F" containing all the code previously in
1771        external_forcing.F, but with new argument list: pass, as new argument,
1772        the current level tendency array to update (instead of a direct update
1773        of the common bloc array). Change the corresponding calls.
1774      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
1775        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
1776    o pkg/seaice/seaice_lsr, a little bit of clean up
1777      - rearrange some code blocks, so that now all calculations for
1778        setting up the right-hand-sides done within one single block
1779        (I find that easier to read and understand)
1780      - rearrange freedrift-code to reduce the number of ifdefs
1781      - adjust some indentations and comments
1782    
1783    checkpoint64z (2014/07/10)
1784    o model/src and several pkgs:
1785      - change argument list of all S/R called from external_forcing.F and
1786        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
1787        to pass, as argument, the current level tendency array to update
1788        (instead of a direct update of the common bloc array).
1789      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
1790      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
1791    o pkg/seaice/seaice_lsr.F
1792      - always initialize local arrays in seaice_lsr_tridiagu/v
1793      - add more local tapes to seaice_lsr_tridiagu/v
1794      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
1795        keep it in bi/bj loop; this seems to be essential
1796      - gradients are still wrong but only by 4-7 orders of magnitude
1797        instead of 15 orders of magnitude, lab_sea improves a little
1798    o pkg/seaice
1799      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
1800        generates unnecessary code in seaice_lsr_ad
1801      - add more store directives in seaice_lsr to avoid unnecessary code
1802        in seaice_lsr_ad
1803      - exclude some residual computations in seaice_lsr when
1804        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
1805        in seaice_lsr_ad
1806      - add more storing, a new tape (model/src/the_main_loop.F) and
1807        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
1808        and klockey should be checked by a specialist)
1809      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
1810        and update lab_sea after previous changes in pkg/seaice below
1811    o pkg/autodiff:
1812      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
1813        viscFacInAd : run time parameters allowing for adjoint switches
1814        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
1815    o pkg/ecco:
1816      - introduce cost_gencost_boxmean.F that computes a box mean
1817        temperature (for use in adjoint sensitivity studies).
1818    o model/src/set_defaults.F : initialize viscFacAdj to 1.
1819    o pkg/mom_common/mom_calc_visc.F:
1820      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
1821    o pkg/seaice/seaice_summary.F:
1822      - statement for SEAICEadjMODE now in autodiff_readparms.F
1823    o pkg/seaice:
1824      - remove some store directives and add new ones in an effort to get
1825        finally rid off the recomputation warnings. This is successful
1826        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
1827        defined (i.e. no extensive recomputation warnings left), but there
1828        are still too many recomputations on the solver iteration level
1829      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
1830      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
1831        SEAICE_SIZE.h
1832      - add a store directive in S/R seaice_calc_viscosities
1833    o pkg/seaice (ITD code):
1834      - fix definition of Hlimit for multi-threaded case
1835      - use double precision arithmetic to compute Hlimit: this affects results;
1836        update output of experiment seaice_itd.
1837    o replace content of verification/seaice_itd
1838      - instead of a 1D column use the configuration of offline_exf_seaice
1839        to test the ice thickness distribution code with ridging
1840      - this is a first shot at this experiment
1841      - change of some defaults of ridging parameters SEAICEhStar (from
1842        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
1843        and lot of new comments.
1844    
1845    checkpoint64y (2014/06/20)
1846    o pkg/seaice/seaice_reg_ridge.F:
1847      - modify the regularization of very small volumes of ice; only check
1848        total volume HEFF, and do not apply correction to individual ice
1849        classes because that leads to funny patterns in the heat and fw-fluxes
1850        into the ocean. Adjust seaice_itd/results/output.txt
1851      - replace nITD by SEAICE_multDim in loop-ranges
1852    o pkg/exf:
1853      - add code to process the case field period = -12. with UV interpolation.
1854      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
1855        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
1856    o verification/global_with_exf:
1857      - switch all fields period to -12. (was previously untested) in input/data.exf
1858        (but keep secondary test ".yearly" unchanged); update the reference output.
1859    o pkg/cal:
1860      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
1861    o pkg/exf:
1862      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
1863        to replace logical switch "exf_verbose"
1864      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
1865    o pkg/sbo:
1866      - update from Katherine Quinn: evaluate mass directly from density and SSH
1867        (budget using Finite Volume method) instead of from bottom pressure.
1868      - allow testreport to collect few selected SBO output ; tested in exp.
1869        global_ocean.90x40x15 (after updating the results, to include SBO output).
1870      - fix some multi-threading issues (in output part).
1871    o model/src & most packages:
1872      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
1873      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
1874        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
1875        "data.{pkg}" exist ; and leave the S/R (return) just after.
1876      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
1877        + call LAND_READPARMS from packages_readparms.F
1878    o pkg/seaice:
1879      - remove code that resets useThSice in S/R seaice_readparms and
1880        replace it by a warning in S/R seaice_check
1881      - remove parameter MULTDIM, replace with nITD and runtime
1882        parameter SEAICE_multDim (still hard-wired to nITD if
1883        SEAICE_ITD is defined)
1884    
1885    checkpoint64x (2014/05/24)
1886    o verification/lab_sea:
1887      - update adjoint and TLM output following changes to pkg/salt_plume
1888      - un-do the update after putting back local recip_Cp in few places.
1889    o pkg/salt_plume: modifications by An Nguyen:
1890      - add capability to do brine rejection (salt-plume) as function of
1891        volume+tracers (instead of only salinity tracer).
1892      - conserve volume by exchanging volume from each kLev to above to
1893        accommodate in-coming brine volume
1894      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
1895      - switch KPP surf buoyancy due to brine forcing to 3-d
1896        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
1897      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
1898      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
1899        in East/West Arctic.
1900    o pkg/sbo:
1901      - incorporate modifications from Katherine Quinn to enable the use of sbo
1902        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
1903        output for future testreport verification (unfinished).
1904    o pkg/atm_phys:
1905      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
1906        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
1907        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
1908    o pkg/seaice
1909      seaice_calc_ice_strength.F: modify expression to avoid divisions
1910        (affects truncation)
1911      seaice_do_ridging.F: clean up the insectarium
1912      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
1913      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
1914      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
1915      - add some debugging information and error messages (warnings)
1916    o model/src: modifications relatd to atmosphere p*:
1917      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
1918      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
1919        of vertical profile tRef in geopotential background and anomaly.
1920      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
1921        and pkg/atm_phys.
1922      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
1923        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
1924    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
1925    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
1926        not used right now, but can be used in BGC packages to fix conservation.
1927    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
1928        other packages too.
1929    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
1930        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
1931    o model/src:
1932      - since we have several heat capacity (even in model/src), define "recip_Cp"
1933        as local variable (no longer in common block) to avoid any confusion.
1934      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
1935    o pkg/exf:
1936      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
1937        air density as function of air Temp, Humidity and atm pressure.
1938    
1939    checkpoint64w (2014/05/02)
1940    o verification:
1941      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
1942        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
1943        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
1944        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
1945        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
1946    o model/src: for atmosphere in p* coords:
1947      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
1948      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
1949        but not yet activated.
1950    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
1951      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
1952      - this changes the results (but not for any verification experiment, because
1953        none tests this), but avoids having an extra field in the restart files
1954    o pkg/seaice: remove global variable TICE (not needed)
1955      - replace by TICES or local variable where necessary (cost_seaice_test,
1956        seaice_diagnostics_state)
1957      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
1958      - use specific read/write routines for reading and writing individual leves
1959        of a multilevel field
1960    o pkg/ctrl & model/inc:
1961      - move additional anomaly fields of control vars (related to options:
1962         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
1963        from DYNVARS.h into new header file: CTRL_FIELDS.h
1964    o pkg/seaice: some small modifications to the ridging code
1965      - make fw2ObyRidge a global variable and add the freshwater flux to
1966        seaice_growth
1967      - pass actual thickness from seaice_prepare_ridging, so that it is
1968        computed only in one place and compute it in the same way as in
1969        seaice_growth
1970      - initialise more fields in seaice_do_ridging that where cause floating
1971        point exceptions over land
1972    o pkg/seaice: preparations for ridging code and first real ridging code
1973      - move most of "PART 1" of S/R seaice_growth into a new and separate
1974        S/R seaice_reg_ridge that will both regularize the state variable after
1975        advection call the actual ridging routine;
1976      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
1977        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
1978      - remove ridging code from seaice_advdiff
1979      - clean up remaining part 1 of seaice_growth in an attempt to make it
1980        more readable (this is probably subjective)
1981      - call seaice_itd_redist once in the initialisation phase to have the initial
1982        conditions in the correct category
1983      - finally: add new ridging routine for ITD code
1984    
1985    checkpoint64v (2014/04/11)
1986    o pkg/ecco:
1987      - add runtime parameters mdt[start,end]date[1,2]
1988      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
1989    o pkg/seaice:
1990      - make deltaC a global variable, so that it can be used in ridging code
1991      - first step towards ridging: introduce new routines that compute
1992        ice strength based on ridging parameters
1993      - add diagnostic for HSNOWITD
1994      - add opnWtrFrac as a global variable (required for ridging scheme)
1995    o pkg/salt_plume + pkg/seaice/seaice_growth.F
1996      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
1997        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
1998    o verification/hs94.1x64x5:
1999      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
2000      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
2001    o autodiff:
2002      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
2003        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
2004        For now, only in pkgs used in verification/hs94.1x64x5.
2005      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
2006        which are specific to TAF/TAMC).
2007      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
2008        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
2009        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
2010      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
2011        building mitgcmuv_ad (make adAll).
2012    o pkg/ecco:
2013      - cost_gencost_seaicev4.F:
2014         reformulate proxy cost as function of sst and local param SEAICE_freeze
2015         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
2016      - add stop statement if old names siv4-[sst,vol] are used
2017      - add snapshots + cost reports for atmospheric longwave
2018      - remove factor 0.1 in front of wtau[u,v]
2019      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
2020         ALLOW_TMI_SST_COST_CONTRIBUTION
2021    o pkg/atm_phys:
2022      - add some diagnostics for Short-wave and for convection S/R.
2023    o pkg/seaice/seaice_growth:
2024      - fix a bug in the lateral melt parameterization for SEAICE_ITD
2025        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
2026      - rearrange loop order for better vector code in the same code block
2027      - rewrite the floeDiameter formula to have fewer divisions
2028      -  (miraculously) none of this changes the results of seaice_itd
2029    o pkg/smooth:
2030      - move param smooth2Ddiffnbt to pkg/ecco
2031    o pkg/salt_plume:
2032      - salt_plume_frac.F:
2033         clean up local param names
2034         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
2035    o pkg/rw:
2036      - add RS version of S/R READ_MFLDS_LEV.
2037    o pkg/streamice:
2038      - fix the restart test by writing/reading pickup_streamice files.
2039    o pkg/seaice:
2040      - refine checks for jfnk-related parameters
2041      - comment out if statement with SEAICEuseIMEX parameter as long as there
2042        is no IMEX code to avoid confusion and surprises
2043    
2044    checkpoint64u (2014/03/07)
2045    o verification/MLAdjust:
2046      - rename secondary test suffix:
2047         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
2048         0.leithD -> AhFlxF  + switch to flux-form
2049         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
2050         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
2051    o pkg/mom_vecinv:
2052      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
2053        to be before mom_calc_visc.F)
2054      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
2055      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
2056        this is simpler for the adjoint and for diagnostics.
2057    o model/src + pkg/momentum:
2058      - add input files for  2-D additional Western and Southern cell-edge wall
2059         (e.g., to add "thin-wall" where it is =1).
2060      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
2061        using 2nd hFacZ that is computed from initial (fix domain) hFac
2062      - known limitations of thin wall implementation: not yet coded for sigma
2063        coords; not working with CD-scheme neither.
2064    o pkg/seaice:
2065      - rename recently introduced parameters from (wrong name) AB to
2066        BDF (backward difference time discretisation)
2067      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
2068    o tools/adjoint_options:
2069      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
2070    
2071    checkpoint64t (2014/02/01)
2072    o pkg/ecco
2073      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
2074        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
2075      - replace hard-coded record number and period which only work for monthly
2076        with read-in runtime param that works for other periods (month,day,year)
2077    o pkg/thsice
2078      - corrected store directive fixes thsice adjoint gradient checks
2079    o genmake2 & testreport:
2080      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
2081        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
2082        Update testreport accordingly. No need to set "export OPENAD=true"
2083        in adjoint_options/adjoint_oad anymore (will be removed later).
2084    o pkg/shelfice:
2085      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
2086        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
2087        so that surface forcing applies to k=kSurf if using pkg/shelfice.
2088    o pkg/ctrl, pkg/grdchk, pkg/ecco:
2089      - Changes to make GENARR more modular (i.e. invisible if not used)
2090    o model/src/temp_integrate.F and salt_integrate.F
2091      - re-include store directives that were removed on Dec 27th.
2092    o model/src/external_forcing_surf.F
2093      - add storage directives for EmPmR and PmEpR to avoid recomputation of
2094        seaice_model in the adjoint that is problematic when seaice_model is
2095        turned off in the adjoint. The resolved issue dated back to July when
2096        EXTERNAL_FORCING_SURF call was moved.
2097        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
2098    o pkg/exf/exf_check.F
2099      - fix a small bug again (originally found by Wentao Liu, now found again)
2100      - streamline error output
2101    o pkg/streamice and aim_v23:
2102      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
2103        Apple's /usr/bin/cpp knows what to do:
2104        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
2105        Target: x86_64-apple-darwin13.0.0
2106    
2107    checkpoint64s (2014/01/05)
2108    o tools/adjoint_options:
2109      - switch to fastopt.net TAF server (instead of default fastopt.de) for
2110        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
2111    o model/src:
2112      - remove some unnecessary TAF storage directives in forward_step.F and
2113        in dynamics.F (note: not always removed by TAF, e.g., double storage
2114        of kappaRU,kappaRV in former version of dynamics.F).
2115    o model/src & pkg/ptracers:
2116      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
2117        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
2118        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
2119      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
2120      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
2121      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
2122    o useSingleCpuInput separates single-CPU input from single-CPU output;
2123        for now only implemented for in exf_interp_read.F
2124    o verification/advect_xy:
2125      - fix missing EXCH call in local version of ini_salt.F and update output.
2126    o momentum diagnostics:
2127      - fix which deltaT is used in Total-Tendency diagnostics.
2128      - fix typo in diagnostics for momentum tendency from AB.
2129    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
2130        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
2131    
2132    checkpoint64r (2013/12/08)
2133    o verification/*/results:
2134      - Update reference output of experiments that were passing with just 13 digits
2135         (make it easier to detect future changes in results)
2136    o model/src & pkg/ptracers:
2137      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
2138        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
2139        to inside ptracers_integrate.F ; remove ptracers_advection.F
2140    o coupling interface pkgs:
2141        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
2142      - change the config check to test the agreement of Ocean Depth
2143        with ATM land/sea mask (instead of ATM orography);
2144      - send to coupler the number of coupler time-steps to do for this run:
2145        this allows to check for consistency and don't need anymore to be
2146        specified in parameter file "data";
2147      in coupler:
2148      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
2149      - improve report to log-file of config setting (pass log-file unit to few S/R)
2150    o pkg/compon_communic:
2151      - add coupling send/receive for non-tiled integer vector;
2152      - add S/R to check and stop if any proc has an error (similar to
2153        eesupp/src/stop_if_error.F but single thread and across Comm_World).
2154    o pkg/exch2:
2155      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
2156        through list of all tiles my proc owns.
2157    o model/src:
2158      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
2159        from rTrans) to simplify dependencies (no need to store rTrans anymore in
2160        calling S/R); this affects AD results at machine truncation level:
2161        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
2162        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
2163    o tools/build_options:
2164      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
2165    o coupling interface pkgs:
2166        [compon_communic, atm_compon_interf & ocn_compon_interf]
2167      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
2168        to each S/R that needs it; remove un-used variables.
2169      - change component tile registration (cpl_register.F in both compon_interf
2170        and mitcomponent_tile_register.F) to pass the full list of tiles
2171        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
2172      - with pkg/exch2: adopt the same convention used for I/O to define mapping
2173        towards coupler global array (unless W2_useE2ioLayOut=F):
2174         a) can now use different tiling between atm & ocn comp.
2175         b) no needs to modify the run-Off map when changing tiling (was needed
2176            even if using the same tiling between atm & ocn).
2177         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
2178            full land tiles); not yet tested.
2179      - check for valid mapping from comp. tile to coupler global array
2180      - improve report of tile registration results to log file.
2181    o pkg/exch2:
2182      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
2183        tile-registration (CPL_REGISTER);
2184      - activate (un-comment) definition and setting of "W2_tileIndex" list to
2185        store the local bi,bj indices of each tile;
2186      - also print bi,bj in local report to log file;
2187      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
2188        Jun 2009 modif of pkg/exch2).
2189    o testing on baudelaire:
2190      - run 2 tests at a time: no significant slow down (since enough cpu) and
2191        get the full set of test done earlier
2192      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
2193    o model/src/thermodynamics.F and routines called from it:
2194      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
2195        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
2196        velocity (outp) by adding bolus velocity.
2197      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
2198        mass transport from velocity + lateral grid cell area
2199      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
2200      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
2201     in thermodynamics.F
2202      - remove k from thermodynamics.F and move it to temp_integrate.F
2203        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
2204        loop).
2205      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
2206        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
2207        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
2208        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
2209      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
2210        global_ocean.90x40x15, tutorial_global_oce_biogeo and
2211        tutorial_tracer_adjsens (+ TLM output).
2212    o tools/OAD_support and (verification/*/) code_oad:
2213      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
2214        module conversion ; remove unneeded CPP_EEOPTIONS.h.
2215      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
2216        version (closer to model/inc/CPP_OPTIONS.h).
2217    o model/src:
2218      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
2219        retired list of parameters (routine FREEZE has been replace by surface
2220        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
2221    o pkg/gmredi:
2222      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
2223        velocity (same scheme but affects machine truncation) for GM_AdvForm.
2224      - update output of FWD experiments: front_relax.bvp,
2225        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
2226    
2227    checkpoint64q (2013/11/17)
2228    o verification:
2229      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
2230        tutorial_global_oce_biogeo and global_ocean.90x40x15.
2231      - generate new output (growth & melt) for seaice_itd experiment after
2232        updating the input pickup_seaice files (previously wrong).
2233    o pkg/cost:
2234      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
2235        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
2236        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
2237          cannot be applied to var in common block).
2238        o allows to get results independent of tile-per-proc setting (if using
2239          slower GLOBAL_SUM_SEND_RECV option).
2240      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
2241        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
2242        forward gradients: update output).
2243      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
2244        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
2245    o pkg/mom_common:
2246      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
2247        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
2248        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
2249        ensure that all field value that are used are set.
2250    o tutorial_deep_convection (smag3d):
2251      - add missing scaling in mom_calc_smag_3d.F;
2252      - set smag3D_coeff in input.smag3d such that results do not change.
2253    o pkg/dic:
2254      - change dic_cost.F to compute cost on each tile first and then apply
2255        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
2256        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
2257      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
2258    o eesupp/src & pkg/mdsio:
2259      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
2260        (from pkg/mdsio) since they are no longer used for tape IO.
2261      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
2262        (+ keep a copy in pkg/atm_ocn_coupler).
2263    o verification/isomip:
2264      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
2265    o tools/build_options:
2266      - optfile linux_amd64_ifort11, fast (no ieee) case:
2267        to get a working restart for all experiments, add "-fp-model source"
2268        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
2269    
2270    checkpoint64p (2013/10/20)
2271    o pkg/autodiff:
2272      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
2273        criteria, return to simple (default) tape IO format.
2274    o pkg/mdsio (+ eesupp/src):
2275      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
2276        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
2277      - fix globalFile and singleCpuIO options using simpler global mapping.
2278      - new pairs of scatter/gather vector S/R (one for each type, generated from
2279        template) corresponding to simpler global mapping.
2280      - adread_write.F: switch to new S/R (but leave old calls commented) and write
2281        to globalFile when parameter globalFiles is set to True.
2282      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
2283    o pkg/autodiff:
2284      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
2285        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
2286        missing, just add a STOP if array type do not match.
2287    o pkg/exf:
2288      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
2289         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
2290         and rename array obsSIce to exf_iceFraction.
2291    o tutorial_deep_convection:
2292      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
2293        for now all in this exp. code dir.
2294      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
2295        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
2296    o eesupp/src:
2297      - added SINGLE_DISK_IO option because reading of parameter files on
2298        very large number of processors did not work with existing set-up
2299    
2300    checkpoint64o (2013/09/25)
2301    o pkg/atm_phys & atm_compon_interf:
2302      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
2303    o tools/build_options:
2304      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
2305        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
2306        remove CPP setting (was identical to genmake2 default).
2307    o pkg/gmredi & model/src: Some updating and work done on the residual model.
2308      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
2309      - fixed up the calculation of the eddy stress and how it is added to the
2310        external forcing via taueddy_external_forcing.F
2311      - at the moment, it is very experimental and only works with the variable eddy
2312        diffusivity calculated in gmredi_k3d.F
2313    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
2314        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
2315    o testreport (& tools/do_tst_2+2):
2316      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
2317    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
2318      - remove CPP='cpp -traditional -P' (this is genmake2 default)
2319      - add switch (for big setups) to use 'medium' memory-model (but leave it
2320        commented out for now). Note: needed with FC 19 to compile big setups.
2321    o pkg/atm_compon_interf:
2322      - regroup per field origin (model & pkgs) the coupling storage routines
2323         (which accumalate in time each coupling field)
2324      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
2325        update accordingly + simplify aim_do_physics.F
2326    
2327    checkpoint64n (2013/08/26)
2328    o pkg/bbl:
2329      - update formulation to reduce dispersion of tracer properties in bbl
2330      - replaced horizontal and vertical transport parameters with velocities
2331      - changes results for verification/global_with_exf.yearly
2332    o verification/halfpipe_streamice:
2333      - change to matrix construction; update both Fwd & AD output.
2334    o verification/tutorial_tracer_adjsens:
2335      - OpenAD test: switch to vector-invariant momentum since fluxform with
2336        rStar causes problems with OpenAD; update output.
2337    o tools:
2338      - genmake2: define a common prefix for all temp-file names ; move them
2339        to local /tmp disk (but would be easy to move them back);
2340      - xmakedepend: apply the same switch for temp-files.
2341    o pkg/offline:
2342      - changes for use with rStar (NLFS): assume that we continue to provide
2343        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
2344        output files) and apply r* scaling at each time-step (function of the time
2345        varying Eta field); use normal pickup files (needed for restart with NLFS).
2346    o adjoint with OpenAD:
2347      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
2348        package openad.  This package has to be compiled for all runs with OpenAD
2349        instead of specifying code_oad_all as a modification directory.
2350      - link the fortran templates from tools/OAD_support to the build directory
2351        for preprocessing to avoid conflicts between different setups compiled
2352        simultaneously and simplify cleanup.
2353    o pkg/exf:
2354      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
2355        main model or other pkgs are exchanged in EXF_MAPFIELDS).
2356    o model/src:
2357      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
2358        (similar to do_fields_blocking_exchanges.F).
2359    o tools/genmake2:
2360      - remove TAF output src code just before calling staf (when not doing a fresh
2361        built, will stop if things go wrong with staf).
2362      - fix target "adobj" (left from TAF version-2 transition)
2363    o pkg/diagnostics:
2364      - add a parameter to track the status of pkg/diagnostics activation;
2365        this replace/extend the use of logical param "settingDiags" (to check
2366        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
2367        New S/R to print error message and stop when pkgStatus is not right.
2368      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
2369    
2370    checkpoint64m (2013/08/13)
2371    o model/inc:
2372      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
2373        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
2374    o pkg/kpp & aim_v23:
2375      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
2376    o pkg/seaice:
2377      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
2378        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
2379      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
2380    o eesupp/src:
2381      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
2382        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
2383    o switch to TAF version-2:
2384      - add flow directives to "freeze" naming convention for ad-routines that
2385        are used in I/O routines of adjoint state and associated common blocks
2386        that are used in adcommon.h (backward compatible with version-1)
2387      - update all ad-optfiles (in tools/adjoint_options + few local to some
2388        verification exp) to switch to latest TAF version (currently 2.5.5);
2389        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
2390        out except for diva).
2391      - the major change with TAF version-2 is that both the differentiated
2392        routines and the forward routines (new) are returned as part of the TAF
2393        output source code. Update genmake2 accordingly.
2394      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
2395        with version-2 when compared to TLM or FWD gradient); other experiments
2396        output show minor changes (machine truncation level); update the few AD &
2397        TLM output with 12 matching digits only (some prior to version-2 switch).
2398    
2399    checkpoint64l (2013/08/05)
2400    o model/src:
2401      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
2402      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
2403        when using TAF but only if using OpenAD.
2404    o pkg/mom_common+fluxform+vecinv:
2405      - always set horiz. viscosity arrays to background value before calling
2406        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
2407        only when using variable horiz. viscosity (useVariableVisc=T);
2408      - simplify mom_vecinv.F (only 1 block for momViscosity).
2409    o pkg/mom_common: variable horiz. viscosity in NH code
2410      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
2411        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
2412      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
2413        useBiharmonicVisc & useVariableVisc.
2414      - fix old bug (already in 1rst implementation of variable horizontal viscosity
2415        in calc_gw.F, version 1.27, 2006/06/20):
2416        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
2417        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
2418      - change background horiz viscosity in vertical momentum (gW) to always be
2419        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
2420        any type of variable viscosity, e.g., viscAh/4Grid)
2421      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
2422        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
2423        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
2424        default viscAh,viscA4 is zero).
2425    o model/src:
2426      - extend length of drC & recip_drC from Nr to Nr+1.
2427    o Divided Adjoint (DIVA) with MPI:
2428      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
2429      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
2430        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
2431    
2432    checkpoint64k (2013/07/23)
2433    o tools/OAD_support:
2434      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
2435        and remove it from genmake2.
2436    o tools/build_options:
2437      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
2438        MPI_HEADER_FILES list (let genmake2 find the missing headers)
2439    o verification/halfpipe_streamice:
2440      - change to driving stress formulation; update both Fwd & AD output.
2441    o tools/genmake2 and Divided Adjoint with MPI:
2442      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
2443      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
2444      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
2445        Makefile, which is set by genmake2, and check which mpi-headers are needed.
2446        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
2447      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
2448    o testreport:
2449      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
2450        perform additional runs (number of additional runs is "add_DIVA_runs" taken
2451        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
2452    o verification/lab_sea (AD test):
2453      - change to test Divided Adjoint Run in this set-up (both standard AD test
2454        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
2455    o pkg atm_ & ocn_compon_interf:
2456      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
2457        staggerTimeStep implementation) and disable (retired) corresponding
2458        parameter.
2459    o pkg/offline:
2460      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
2461      - add S/R OFFLINE_CHECK to print offline parameter summary
2462        and stop if loading a file that is not used;
2463      - enable to calculate GMRedi tensor, KPP mixing and convective index
2464        when the corresponding file(s) is/are not specified (but pkg is used).
2465      - comment out resetting of monitorFreq (to endTime) since it still useful
2466        for monitoring CFL numbers and checking offline fields.
2467    o OpenAD:
2468      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
2469        smaller standard output) and generate new (smaller) output (on baudelaire
2470        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
2471    o model/src:
2472      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
2473        (where external_forcing_adjust was called) and change list of arguments;
2474      - merge external_forcing_adjust.F into external_forcing_surf.F
2475      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
2476        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
2477        previously in file "balance_relax.F", now removed); remove corresponding
2478        arrays in FFIELDS.h.
2479      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
2480        a hack for getting back surfaceForcingS (loaded from file) when using
2481        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
2482      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
2483        (was getting only 11 digits for AD-grad, due to different truncation
2484         error in AD code).
2485    
2486    checkpoint64j (2013/07/04)
2487    o pkg/offline:
2488      - to enable the use of other features with pkg offline (e.g., obcs),
2489        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
2490      - comment out "allowFreezing" (now active) in 2 offline testing exp.
2491    o pkg/exf ALLOW_RUNOFTEMP
2492      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
2493      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
2494      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
2495    o pkg/atm_phys:
2496      - allows to add some damping on uVel,vVel (strength only function of k).
2497    o verification, ad-tests:
2498      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
2499        global_ocean_ebm and offline_exf_seaice.thsice.
2500    o verification/halfpipe_streamice:
2501      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
2502        flux input boundary conditions to be ignored; a fix for this bug changed
2503        verification results for forward test.
2504      - add adjoint test.
2505    o pkg/ptracers:
2506      - allow to restart without SOM pickup (resetting SOM to zero).
2507    o pkg/gmredi:
2508      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
2509      - It uses mixing length theory and suppression by steering level effects to
2510        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
2511        to JPO, for more details).
2512      - It also uses the diffusivity to calculate an eddy induced streamfunction
2513        based on a PV closure (rather than a buoyancy closure as in GM).
2514      - New files added to pkg/gmredi:
2515        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
2516          induced overturning streamfunction (called from gmredi_calc_tensor)
2517        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
2518          for use in gmredi_k3d
2519        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
2520          the eddy diffusivity
2521    
2522    checkpoint64i (2013/06/18)
2523    o pkg/cheapaml:
2524      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
2525        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
2526        with pkg/cheapaml.
2527    o utils/python: add subpackage for cubed sphere function, first example is
2528        simple cs.pcol to plot 2D fields on a map
2529    o pkg/streamice:
2530      - This is a new package in MITgcm, which solves dynamic equations for ice
2531         sheets and ice streams
2532      - At the moment it is independent of atmosphere/ocean dynamics, or any
2533        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
2534        ed that this will change)
2535      - There is a new verification exercise that tests it, halfpipe_streamice,
2536        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
2537        rectangular embayment
2538      - halfpipe_streamice is forward-only for now, will have TAF test soon
2539      - for questions, email dgoldber@mit.edu
2540    o pkg/thsice:
2541      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
2542        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
2543      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
2544         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
2545      - allow precip from pkg/cheapaml to make snow over seaice.
2546    o pkg/cfc:
2547      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
2548      - remove atmos CFC 2-D arrays from common bloc (now local variables)
2549      - change some hard-coded constant to run time parameter for reading and
2550        and interpolating atmospheric CFC ; keep same default as previously.
2551      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
2552      - put arguments in standard order: myTime, myIter, myThid
2553      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
2554        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
2555      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
2556      - new routine to print summary of CFC params and check for consistency.
2557    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
2558      similar to thsice_advdiff.
2559      Note that for the B-grid case the routine parameters uc/vc are overwritten.
2560    o pkg/cfc:
2561      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
2562        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
2563      - fix interpolation of atmphspheric CFC between Sorthern and Northern
2564        hemisphere value.
2565    o pkg/seaice:
2566      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
2567    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
2568                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
2569      - requires an additional time level that is stored in the pickup
2570      - you can start with AB2 from a pickup without this time level with
2571        pickupStrictlyMatch = .false.
2572    
2573    checkpoint64h (2013/05/26)
2574    o pkg/cheapaml:
2575      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
2576        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
2577      - consistent treatment of uWind,vWind location: assume everywhere in
2578        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
2579        (Note: was already the case for Tair,Qair advection);
2580        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
2581      - compute diabatic forcing only in the interior (excluding overlap regions)
2582      - fill in array "Qsw" (for short-wave heating);
2583      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
2584        before any update (consistent with MITgcm state var diagnostics);
2585      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
2586        non periodic ; + adjusted for uWind,vWind (C-grid).
2587    o pkg/seaice:
2588      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
2589        add explicitly pkg/exf in experiments that currently use pkg/seaice.
2590      - allows to compile pkg/seaice without pkg/exf.
2591    o tools/OAD_support:
2592      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
2593        of array "ourStepOf" in function rvNextAction (revolve.F90).
2594    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
2595      - change pkg name (to be used with other atmospheric physics pkg)
2596        but by-pass CVS when making the new pkg so that we keep the CVS history.
2597    o pkg/offline:
2598      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
2599        (previously called from pkg/dic_surfforcing_init.F)
2600    o model/src:
2601      - re-order sequence of calls within packages_init_variables.F, using
2602        standard order, except for:
2603         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
2604         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
2605    o new pkg: atm_phys
2606      - add entry point and source code (previously in contrib
2607          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
2608        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
2609      - re-order sequence of calls within packages_readparms.F,
2610         packages_init_fixed.F and packages_write_pickup.F
2611        (but skip packages_init_variables.F because of TAF issues).
2612      - update contrib/*/atm_gray/ experiment.
2613    o pkg/seaice (ITD code):
2614      - simplify and fix the writing of pickup-files for ITD case
2615    o pkg/seaice (ITD code):
2616      - introduce floe size dependent lateral melt for ITD case;
2617      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
2618      - update seaice_itd experiment main output.
2619    o pkg/thsice:
2620      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
2621        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
2622        changed accordingly pkg/atm2d.
2623    
2624    checkpoint64g (2013/05/01)
2625    o pkg/exf ALLOW_RUNOFTEMP
2626      - if defined,  river and glacier runoff temperature can be read-in from
2627        runoftempfile; runoftempfile needs to have same format as runofffile
2628    o pkg/thsice (& pkg/bulk_force):
2629      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
2630        for energy content of Precip + RunOff & Evap (like with pkg/exf).
2631      - change computation domain to always be the interior (without overlap).
2632      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
2633    o verification/tutorial_global_oce_biogeo:
2634      - add preliminary OpenAD setup (still has problems)
2635    o pkg/seaice:
2636      - turn some parameters for choosing the convergence criterion of
2637        the inexact Newton method (JFNK) into runtime parameters for convenience
2638      - clean up seaice_calc_viscosities.F: remove/retire two options for
2639        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
2640        the results of lab_sea/input because a division has been replaced by
2641        a multiplication with the reciprocal (sumNorm)
2642      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
2643        convergence of solver (changes results, of course), and to test some
2644        new features
2645    o model/src:
2646      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
2647      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
2648      - move forcing adjustment (balancing surface forcing) in specific S/R
2649        where might also be applied exchanges (if needed) to forcing arrays.
2650    o pkg/shelfice:
2651      - allow to specify the Ice-Shelf mass per unit area (instead of
2652        shelficeLoadAnomaly) and do the conversion from one to the other
2653      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
2654        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
2655        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
2656        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
2657      - update isomip experiment forward output (get machine truncation error
2658        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
2659    o verification/offline_exf_seaice:
2660      revise data.seaice in input.thermo and input_ad and update results accordingly
2661        HO = 0.2, SEAICE_areaLossFormula = 2,
2662        SEAICE_growMeltByConv = .TRUE.,
2663        SEAICE_doOpenWaterMelt = .TRUE.,
2664      Improve consistency with input.thsice and fix the spurious 500m ice corners
2665    o verification/global_ocean.cs32x15:
2666      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
2667        in icedyn (thsice+seaice-dyn) test and update output.
2668    o verification/offline_exf_seaice:
2669      - adjust list of tested variables (with testreport) and update
2670        standard test output with better slection of monitored fields.
2671    o pkg/cd_code:
2672      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
2673        experiment lab_sea.hb87
2674    o tools/genmake2:
2675      - change default makedepend from the system default to tools/xmakedepend:
2676        When no makedepend is specified, select tools/xmakedepend it the test pass,
2677        otherwise select the system default (if exist and pass the test) or
2678        try to build cyrus-makedepend ; stop if none of the 3 works.
2679    o pkg/exf & pkg/thsice:
2680      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
2681        for energy content of Precip + RunOff & Evap. Assumes:
2682       1) Rain has same temp as Air.
2683       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
2684       3) Run-Off comes at the temp of surface water (with same Cp)
2685       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
2686        put directly into Latent Heat flux & should use water-vapor heat capacity.
2687       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
2688        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
2689    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
2690        (compile when SEAICE_ALLOW_JFNK is defined)
2691    o pkg/thsice:
2692      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
2693        implementation): move THSICE_AVE call after the advection (called directly
2694        from thsice_do_advect.F).
2695    o verification/global_ocean.90x40x15 and OpenAD:
2696      New experiment for OpenAD is identical to the one in input_ad except that
2697        multiDimAdvection=.FALSE.,
2698      There is still an issue with this.
2699    o pkg/thsice:
2700      - account for ice velocity (ocean relative velocity) in turbulent heat flux
2701        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
2702        and offline_exf_seaice (main test).
2703    
2704    checkpoint64f (2013/03/31)
2705    o verification/OpenAD:
2706      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
2707    o verification/isomip, pkg/shelfice and OpenAD:
2708      - add OpenAD setup to this exp and make shelfice package work with OpenAD
2709    o verification/tutorial_global_oce_biogeo:
2710      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
2711    o verification/offline_exf_seaice:
2712      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
2713    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
2714      - add OpenAD setup to this exp and make ptracers package work with OpenAD
2715    o pkg/seaice/seaice_evp.F:
2716       mask the asymmetric contribution of the ice-ocean stress (when
2717       the turningAngle is non-zero) over open water to avoid stripes
2718       in the EVP-solutions after many EVP-substeps. This does not change
2719       the verification experiment (because turningAngle=0 in that experiment),
2720       but will affect other EVP solutions with turningAngle.ne.0
2721    o verification, AD & TLM output:
2722      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
2723        additions and multiplications which affect results at machine truncation
2724        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
2725        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
2726        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
2727        digits of matching.
2728    o pkg/seaice:
2729       modify lsr-algorithm so that it vectorizes AND converges by using a
2730       "zebra" method: split vector loop into two with step size 2; this
2731       solves a general convergence problem for the JFNK solver on a vector
2732       computer. It has the potential to even improve convergence for
2733       non-vector machines, but it does change the results so it is turned
2734       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
2735       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
2736    
2737    checkpoint64e (2013/03/05)
2738    o pkg/ecco and several verification experiments:
2739       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
2740       from ecco package, and revert to unified routine in model/src/
2741       Adjust verification experiments accordingly, especially gloal_oce_llc90
2742       Should conclude long-standing work by Gael to reconsile the_main_loop with
2743       ECCO and will enable OpenAD's revolve loop in ECCO setup.
2744    o pkg/generic_advdiff:
2745      - implement compressible flow method for multi-dim advection (similar to
2746        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
2747        TAF generates many recomputations) to use it; no yet coded with implicit
2748        vertical advection.
2749      - change experiment advect_cs (new output) and advect_xy (same output)
2750        to test compressible flow multi-dim advection.
2751    o pkg/generic_advdiff:
2752      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
2753        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
2754    o pkg/seaice:
2755      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
2756        bug affects two verification experiments (lab_sea and lab_sea.hb87),
2757        recover old (wrong) results by setting noSlipFac = 2. in
2758        seaice_calc_strainrates.F;
2759      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
2760      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
2761        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
2762      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
2763    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
2764      - new subroutines seaice_lsr_tridiagu/v
2765      - introduce loop bounds i/jmin/max to be able to use a restricted
2766        additive Schwarz method, but not used for now.
2767      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
2768      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
2769    o OpenAD support
2770       Reorganize S/R call for overall time-stepping loop to facilitate
2771       OpenAD revolve loop replacement
2772       (new S/R main_do_loop.F)
2773    o model/src:
2774      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
2775      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
2776        ADAMS_BASHFORTH2.
2777    o pkg/cheapaml:
2778      - add new parameter (default=F, same as before) to disable full domain
2779        (including land) periodicity in X & Y dir.
2780      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
2781        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
2782        into single S/R CHEAPAML_TIMESTEP.
2783    
2784    checkpoint64d (2013/02/17)
2785    o pkg/monitor (angular momentum):
2786      - do not add Eta contribution to the total AM if using rigid-lid;
2787      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
2788      - horizontal discretisation: compute Zonal wind contribution separately for
2789        each component (instead of from cell centered averaged) and use the 4
2790        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
2791      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
2792        FreeSurf) if using vectorInvariant momentum.
2793    o model/src (horizontal grid):
2794      - move initialisation of all horizontal grid arrays to null value
2795        from specific horizontal grid S/R to main S/R INI_GRID;
2796      - add 2 new arrays to project model C-grid velocity on to zonal direction
2797        (similar to AngleCosC & -AngleSinC but at U and V point location) and
2798        compute them in S/R CALC_GRID_ANGLES.
2799    o pkg/seaice: replace a hard coded parameter by a runtime parameter
2800        SEAICE_JFNK_tolIter
2801    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
2802        preconditioner for JFNK (run LSR into the overlaps as far as possible,
2803        i.e OLx/y-2, but overwrite the solution in the overlaps)
2804      - extend loop range in seaice_calc_viscosity
2805      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
2806      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
2807      - slightly modify loops in tridiagonal solver lsr-preconditioner
2808      - by default remove the extra exchange in seaice_preconditioner with a
2809        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
2810      - modify offline_exf_seaice so that old results without RAS are reproduced
2811        for output.dyn_jfnk.txt
2812      in seaice_fgmres.F (unrelated to RAS)
2813      - add a cpp-flag option for a re-ordered mapping (potentially more
2814        efficient), but because this changes the results, turn it off by
2815        default
2816      - replace the save statement by local common blocks
2817    o utils/matlab:
2818      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
2819      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
2820        instead of local script "load_cs.m".
2821    o pkg/seaice:
2822      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
2823        to the scalarProductMetric and the unrolling. By chance this does not
2824        change the verification experiment, because of the particular domain
2825        decomposition
2826    o pkg/diagnostics:
2827      - change default missing_value from UNSET_RL to -999.
2828    o pkg/layers: improve vectorization of layers_fluxcalc.F
2829      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
2830        time spent in this routine by more than a factor of 3 on an NEC-SX8
2831      - step 2: replace search algorithm by a bisection algorithm found in
2832        Press et al. Numerical Recipes in Fortran. This algorithm can be
2833        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
2834        For now, use this algorithm only for TARGET_NEC_SX defined.
2835      - moved the search algorithm into a separate subroutine, that is kept
2836        within the same file for automatic inlining.
2837      - modified catching potential errors
2838    o pkg/ecco:
2839      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
2840    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
2841      - modifications for ALLOW_GENTIM2D_CONTROL
2842      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
2843      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
2844      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
2845      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
2846    o model/src:
2847      - account for moist thermodynamics in (dry) potential temperature equation;
2848        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
2849        and cpl_aim+ocn.
2850      - also switch to standard compiler (gfortran, was using ifort previously)
2851        for fizhi-cs experiments reference output.
2852    o pkg/ctrl:
2853      - 1st step toward generic time-varying control variable (2D) via CPP option
2854        ALLOW_GENTIM2D_CONTROL
2855      - note new namelist ctrl_nml_genarr in data.ctrl
2856    o verification/global_ocean.cs32x15:
2857      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
2858        thsice calling sequence and update "output.icedyn.txt" output file.
2859    o pkg/ptracers:
2860      - from Ryan A.: code to allow to restart a tracer at regular time interval
2861        specifying a reset frequency and a reset-phase (for each tracers).
2862    o pkg/thsice:
2863      - implement new sequence of calls for thsice+seaice:
2864          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
2865          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
2866      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
2867        in CPP_OPTIONS.h) to recover old sequence;
2868      - update diagnostics for Intermediate State thsice diagnostics: now filled
2869        just before advection (instead of just after advection in old sequence);
2870      - update output of experiment offline_exf_seaice (standard test);
2871      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
2872        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
2873    o pkg/aim_v23:
2874      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
2875      - use standard pkg/mdsio routines to read & write CO2 pickup file;
2876      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
2877      - Implement new sequence of calls for seaice advection (with thsice and
2878        seaice diffusion): do ice advection after ice-Thermodynamic (previously
2879        was done before); change aim_do_physics.F (split the bi,bj loops block);
2880      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
2881    o pkg/thsice:
2882      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
2883        where just seaice diffusion is used without seaice-dynamics.
2884    
2885    checkpoint64c (2013/01/18)
2886    o pkg/seaice:
2887      - add a parameter JFNKres_tFac that can replace JFNKres_t
2888        (= JFNKres_tFac*JFNKresidual before JFNK solver)
2889      - add a line search option to the JFNK solver
2890      - move update of u/vIce and computation of initial residual into a separate
2891        routine (same file); makes the code a little easier to read (?)
2892      - the line search requires computation of the residual and for some reason
2893        I cannot do the update of u/vIce at the beginning of the Newton loop
2894        without changing the results, so we move computation of the new residual
2895        also to the end of the Newton loop, even without the line search
2896    o pkg/mdsio:
2897      - write missing value (corresponding to undefined array value) to meta files;
2898        skip this if missing value is one (UNSET_RL would be a better value for the
2899        case of undefined missing value but it's current the default missing-value);
2900        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
2901    o pkg/exf & thsice:
2902      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
2903        diagnostics) even when SHORTWAVE_HEATING is #undef;
2904    o verification/cfc_example:
2905      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
2906        illustrate how to use it).
2907    o verification/offline_exf_seaice:
2908      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
2909        files to only one time-record.
2910      in input.thermo: narrow the 2 bands of low initial ice-concentration near
2911        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
2912        snapshot output; same mcPheePiston value as in thsice with
2913        surf-current=0.2m/s.
2914      in input.thsice: similar set-up as in input.thermo (channel with same seaice
2915        initial conditions).
2916    o verification/cfc_example:
2917      - update file "data" with more standard choice (default rotationPeriod,
2918        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
2919        set deltaTFreeSurf to deltaTtracer) and update the output.
2920    o pkg/layers:
2921      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
2922      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
2923    o verification/offline_exf_seaice:
2924      - set all {field}period to zero for constant-in-time forcing (not tested
2925        anywhere else).
2926    o verification/offline_exf_seaice:
2927      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
2928      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
2929    o model/src:
2930      - implement Finite-Volume method for (hydrostatic) presure gradient
2931        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
2932    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
2933      - In order to be compatible with the default EVP code, this requires changing
2934        the EVP code around a little; and because any small change immediately
2935        breaks the lab_sea.hb87 verification experiment, the reference output is
2936        updated two times (each time the remaining aggrement was only 2 digits):
2937        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
2938        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
2939        The adjoint test lab_sea.evp also needed to be updated.
2940      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
2941        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
2942        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
2943        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
2944        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
2945        kept obscure, because I need to test it a little more.
2946    o pkg/cheapaml:
2947      - fix few incorrect type (_RL/_RS) in subroutine calls.
2948    o pkg/seaice:
2949      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
2950        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
2951    o model/src:
2952      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
2953        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
2954        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
2955    o pkg/cheapaml:
2956      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
2957        update output of experiment cheapAML_box.
2958      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
2959        and set them only in one place (cheapaml_readparms.F).
2960      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
2961      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
2962        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
2963    o model/src/the_main_loop.F:
2964      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
2965    o pkg/seaice:
2966      - remove legacy branch code.
2967      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
2968    o verification/*/code*/SEAICE_OPTIONS.h:
2969      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
2970        SEAICE_CAP_HEFF).
2971    o pkg/cheapaml:
2972      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
2973        to load new forcing fields.
2974      - add missing "_d 0" where it's needed; + some editing (improve indentation).
2975      - remove switch to "-r8" compiler option (no longer needed) in verification
2976        cheapAML_box, keep same output (small trucation error differences).
2977    o verification/offline_exf_seaice:
2978      - add thermodynamics only test.
2979    o verification/cheapAML_box:
2980      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
2981        keep same output (same 14 digits for cg2d).
2982      - switch on "-r8" compiler option (some numerical values are missing
2983        the "_d 0") and update output (only 6 digits for cg2d were preserved).
2984    
2985    checkpoint64b (2012/12/24)
2986    o pkg/cheapaml:
2987      - remove un-used variables (Qnet,EmPmR) from pickup files.
2988      - store tendency of advected variables into cheapaml pickup file
2989        and fix the AB-2 restart.
2990    o verification/offline_exf_seaice and lab_sea adjoint:
2991      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
2992      - switch to 4 time steps in offline, consistent with lab_sea.
2993      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
2994      - update results after change of experiment seaice.
2995    o pkg/seaice:
2996      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
2997        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
2998        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
2999        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
3000    o model/src:
3001      - add run-time parameter to select CG2D solver minimum-residual solution
3002        (in case of a poor convergence).
3003    o pkg/seaice/seaice_lsr.F
3004      - move calculation of matrix coefficients into new
3005        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
3006        file; the main purpose of this change is to be able to reuse the code
3007        in S/R SEAICE_PRECONDITIONER
3008      - modify the computation of the residual so that the mass of sea-ice
3009        is not used twice; this simplifies the calculations, but since
3010        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
3011        not tested in testreport---this does not affect the testreport results.
3012    o verification/seaice_obcs:
3013      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
3014        verification/lab_sea/input.salt_plume; changes results/output.txt*
3015    o model/src:
3016      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
3017    o pkg/seaice:
3018      - improve description of parameters in seaice_fgmres.F and start
3019        cleaning up the code
3020      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
3021        second argument
3022      - add a metric based on grid cell area to SEAICE_SCALPROD; update
3023        results of offline_exf_seaice.dyn_jfnk
3024      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
3025    o pkg/aim_v23:
3026      - fix an other bug in dissipation heating (grid-cell area was missing).
3027    o model/src + pkg/seaice:
3028      - add global (multi-tile) linear solver for pair of tri-diagonal system
3029        along X and Y lines, respectively for U and V component.
3030        Note: 1) MPI and cube-exchange not yet coded.
3031            2) probably not accurate for poorly conditioned / large size problem.
3032      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
3033        default: not compiled and not used.
3034    o pkg/seaice:
3035      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
3036        introduce bi/bj loops and use global_sum_tile_rl instead of
3037        mpi_allreduce in seaice_fgmres.F
3038      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
3039      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
3040      - add a verification experiment for JFNK in offline_exf_seaice
3041    o verification:
3042      - change (for now, only fwd test) offline_exf_seaice experiment:
3043        use a re-entrant channel with idealized coastline (trapezoidal shape)
3044        at southern boundary to explore seaice dynamics and thermodynamics
3045        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
3046        secondary test (input.thsice) use thermodynamics only with SST relaxation.
3047      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
3048    o pkg/exf:
3049      - disable "sstExtrapol" when Nr=1
3050    o verification:
3051      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
3052        to test pkg/cheapaml.
3053    o pkg/aim_v23 & pkg/shap_filt:
3054      - fix dissipation heating (erroneous gravity multiplication factor).
3055    o pkg/seaice:
3056      - remove unused field pressPre from jfnk solver
3057      - rename two subroutines in seaice_preconditioner.F
3058    o eesupp/src:
3059       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
3060    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
3061       - remove wrong parts of the rhs and the lhs (were in there
3062         because I did not understand the concept of this preconditioner)
3063       - add an exchange between u- and v-sweep. This increases communication
3064         by a factor of two but improves the convergence of jfnk. Ideally,
3065         one would like the u- and v-sweep to be independent. So far within
3066         undocumented ifdefs
3067       - reorganize the extra computations for printing the residuals
3068    o tools/genmake2:
3069      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
3070        since it's not necessary (and was preventing to use MNC in some cases).
3071    
3072    checkpoint64a (2012/11/16)
3073    o pkg/autodiff:
3074      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
3075        autodiff_readparms.F no longer depends on calling order (within
3076        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
3077        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
3078        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
3079    o pkg/obcs:
3080      - adding tidal velocity forcing capability to obcs
3081        for usage example, see verification/seaice_obcs/input.tides
3082    o pkg/seaice:
3083      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
3084        SEAICE_LSRrelaxU/V
3085      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
3086    o pkg/aim_v23:
3087      - implement heating from friction (bottom friction and stratospheric drag).
3088    o pkg/shap_filt:
3089      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
3090        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
3091    o model/src:
3092      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
3093        time-constant addMass field from file (addMassFile);
3094      - support for heating due to friction (and Kinetic Energy dissipation):
3095        add option, run-time switch and 3-D field array + support code ; each pkg
3096        or S/R can add heating contribution (if there is a sink of KE); the sum is
3097        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
3098    o pkg/seaice:
3099      - complete merge of ITD code into seaice_growth.F
3100        from MITgcm_contrib/torge/itd/code/
3101        no verification so far, but Torge Martin tested
3102        "1-D test case and Beaufort set up;
3103        deliver okay results after 1 model year."
3104      - complete merge of SEAICE_SIZE.h into all relevant routines
3105      - move computation of eta at Z-points into calc_viscosities
3106        + introduce global field etaZ
3107        + add different methods for computing etaZ, for now the old
3108          method (simple averages of eta to Z-points) is hardwired
3109        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
3110          seaice_preconditioner
3111      - simplify computations for SEAICE_ZETA_SMOOTHREG
3112      - seaice_preconditioner:
3113        + replace one remaining press by pressLoc (mistake)
3114        + adjust printing of residuals
3115      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
3116        + add (SEAICE.h) and rename some counters (initiliased in
3117          seaice_init_fixed.F)
3118        + add _BEGIN/END_MASTER (myThid)  around print statements
3119        + print total number of iterations and failures over SEAICE_monFreq
3120          interval to STDOUT
3121      - move control over output-messages by fgmres to seaice_jfnk to save
3122        some operations
3123      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
3124        in order to make restarts with sol .ne. zero (fgmres with restarts)
3125        (seaice_jfnk.F, seaice_fgmres.F)
3126      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
3127        a serious convergence problem when open boundaries are involved
3128    o pkg/ggl90: fix computation of control volumes for the case of
3129      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
3130      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
3131    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
3132    o pkg/autodiff
3133      - Add inAdMode switch for SEAICEuseDYNAMICS:
3134        SEAICEuseDYNAMICSinAdMode
3135        (extend logic in ADAUTODIFF_INADMODE_SET)
3136    o pkg/seaice
3137      - Step 1 of merging ice-thickness distribution (ITD) code from
3138        MITgcm_contrib/torge/itd/ (author: Torge Martin)
3139        The code implements concept laid out in Thorndike et al. (1975);
3140        code is enabled via CPP flag SEAICE_ITD
3141        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
3142        code is not complete yet!!
3143      - SEAICE_SIZE.h now included in almost all seaice routines
3144    o verification (using seaice):
3145      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
3146        global_ocean.cs32x15.seaice ; update results.
3147      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
3148      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
3149        offline_exf_seaice (previously compiling B-grid).
3150    o pkg/exf:
3151      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
3152        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
3153        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
3154    o pkg/layers (adjust changes from Sept 19):
3155      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
3156        this allows to remove "layers_maxNum" dimension from all layers arrays.
3157    o pkg/layers (adjust changes from Sept 19):
3158      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
3159      - snap-shot extended to all type of layers (not just the 1rst type);
3160      - remove layers variables when corresponding CPP option is undef.
3161    o pkg/layers:
3162      - rename pkg/layers variable and add new output (layer exist & un-weighted
3163        velocity in layer)
3164    o pkg/seaice:
3165      - simplify (?) ocean-drag coefficent computations by using
3166        the same routine in all three solvers (saves some code lines)
3167      - remove global fields DRAGA and DRAGS from C-grid code and
3168        declare them locally in lsr.F (the only place where they are
3169        still used)
3170      - update AD output of lab_sea.evp (very sensitive anyway).
3171    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
3172      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
3173      and SEAICEuseJFNK=.true. A few things to note:
3174      - involves a FGMRES, that is parallel but very inefficient,
3175        because of many scalar products (global sums) in the Gram-Schmidt
3176        orthogonalization method. Needs to be replaced. Original code
3177        from J.-F. Lemieux
3178      - preconditioner for FGMRES is a stripped down version of LSOR
3179      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
3180        preconditioner. For the preconditioner, the default is set to 10.
3181      - Jacobian times vector is computed with finite differences
3182      - marginally related to JFNK-solver: add a smooth regularization for
3183        zeta with tanh that will improve convergence (Lemieux and Tremblay,
3184        2009) for any implicit solver (not implemented for EVP because EVP
3185        does not need this regularization in the first place). Define
3186        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
3187    o eesupp/src:
3188      - check in genmake2 that intrinsic S/R flush is available.
3189      - add S/R to flush IO unit (if intrinsic S/R flush is available)
3190      - flush standard & error msg unit before MPI termination
3191      - if debugMode, flush IO unit after printing msg
3192    o pkg/ctrl:
3193      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
3194        to ctrl_set_unpack_xyz.
3195    
3196    checkpoint64 (2012/10/09)
3197    o pkg/shelfice
3198      - in mom_fluxform.F, mom_vecinv.F:
3199        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
3200        Bug fix KappaRU -> KappaRV
3201        does not change verification/isomip but may change other setups
3202        (presumably constant KappaRU=KappaRV)
3203      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
3204    o pkg/obcs:
3205      - fixed some indexing bugs in obcs_seaice_sponge.F
3206      - added obcs relaxation subroutines for HSALT and HSNOW
3207      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
3208    o pkg/seaice:
3209      - add "multicategory" parameterization for snow in analogy to ice,
3210        default is off for now.
3211    o pkg/obcs:
3212      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
3213        see verification/seaice_obcs/input.seaiceSponge for example application.
3214      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
3215        index setting by master-thread. This fix multi-threads Pb in previous modifs.
3216    o pkg/layers :
3217      - add diagnostics to pkg/layers
3218      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
3219        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
3220    o pkg/generic_advdiff/gad_implicit_r.F :
3221      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
3222    o pkg/seaice/seaice_growth.F:
3223      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
3224    o pkg/obcs:
3225      - change default setting of OBCS_UVICE_OLD from defined to undef;
3226      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
3227        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
3228      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
3229      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
3230        with Southern & Western OB at a tile edge (at least in a simple set-up).
3231    o pkg/obcs:
3232      - change settings of OB index in case OB coincides with tile edge (shared by
3233        2 tiles), so that common OB location is registered by both tiles (instead of
3234        only 1). However, for Southern and Western OB, index value = 0 is not
3235        recognized as valid OB index (=default null value) and needs to be fixed.
3236      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
3237      - new parameter "OB_indexNone" for null index value (for now, still zero)
3238        to replace hard-coded null index value of zero.
3239    o pkg/exch2:
3240      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
3241        always check buffer-size (but outside the loop); move checking for valid
3242        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
3243        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
3244    o pkg/ctrl (pack & unpack):
3245      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
3246        (locally defined) for different variables (+ remove the variable-specific
3247        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
3248        (to be extended to other local file names in ctrl.h).
3249    o pkg/flt:
3250      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
3251    o pkg/mdsio:
3252      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
3253    o tools/genmake2:
3254      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
3255        (added by Alistair in version 1.51 for building without make depend);
3256      - remove Header files list (H_SRC_FILES) from the dependence of targets
3257         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
3258        place in version 1.23): this save going through staf when unrelated header
3259        file has been modified.
3260       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
3261        "make depend" step, still need to do "make links" before "make adtaf".
3262    o eesupp/src (+ few pkg src files) & genmake2:
3263      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
3264      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
3265      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
3266         upper/lower case ; account for space between "#" and undef/define)
3267    o pkg/flt (with exch2):
3268      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
3269      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
3270    
3271    checkpoint63s (2012/09/05)
3272    o pkg/ecco:
3273      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
3274      - add more relevant #ifdef ALLOW_SMOOTH ones.
3275      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
3276    o pkg/ctrl:
3277      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
3278        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
3279      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
3280        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
3281        ctrlSmoothCorrel3D (new).
3282        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
3283      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
3284      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
3285        controls when useAtmWind, and vice versa.
3286      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
3287      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
3288          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
3289      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
3290          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
3291      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
3292        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
3293    o pkg/smooth:
3294      - remove un-necessary includes.
3295      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
3296        Those CPP options were never defined, and not necessary.
3297    o model/src:
3298      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
3299      - standard treatment of useSMOOTH.
3300    o pkg/autodiff:
3301      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
3302        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
3303    o pkg/exch2:
3304      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
3305        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
3306      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
3307        and tiles to process mapping.
3308      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
3309        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
3310        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
3311        from w2_eeboot.F to w2_readparms.F.
3312    o eesupp/src:
3313      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
3314        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
3315        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
3316      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
3317        is defined (remove condition on usingMPI) to match cases where MPI_INIT
3318        has been called.
3319      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
3320      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
3321        (so that on 1 proc, get same myPid independently of usingMPI)
3322      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
3323        useCubedSphereExchange with EXCH-1 (safer).
3324      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
3325    o pkg/ggl90:
3326      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
3327        used in ALLOW_GGL90_SMOOTH code.
3328    o pkg/flt:
3329      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
3330        floats at the Southern end of the domain).
3331    o eesupp/inc:
3332      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
3333        but not used (and not to be used) anywhere, just for documentation.
3334    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
3335      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
3336        a) can damage previously written records in any other multi-record files.
3337        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
3338    o tools/genmake2:
3339      - define variable MAKE within Makefile and use it in place of 'make';
3340      - update AD_CONFIG.h (if needed) before building any of the executable
3341        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
3342        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
3343      - always print usual warning comment 'this file is automatically generated'
3344        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
3345    o pkg/cheapaml:
3346      - updated to correspond to the code used in accepted paper (Nico Wienders).
3347    o pkg/exf:
3348        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
3349        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
3350        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
3351    o pkg/exf, autodiff, ctrl, ecco and seaice:
3352        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
3353    o pkg/ctrl, ecco:
3354        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
3355        Depending on useAtmWind, one is inactive, and the other is active (see
3356        exf_getffields.F/exf_getsurfacefluxes.F).
3357    o tools/genmake2:
3358      - improve error msg when failing in 2nd test of check_for_broken_Ff
3359      - fix option '-makefile' short-name (-mf according to genmake2 -help)
3360      - source local config file "genmake_local" just after processing the genmake2
3361        command arguments (previously done before processing arg).
3362    o pkg/grdchk:
3363      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
3364        to this routine from cost_final has been dropped in g_cost_final)
3365      - improve printed information (more explicit msg, no longer using "print *,"
3366         fix fcpertminus printed value).
3367    o model/src:
3368      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
3369        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
3370        this prevents getting cost-funct reset in adinitialise_varia recomputations.
3371    o pkg/dic:
3372      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
3373        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
3374    o pkg/grdchk:
3375      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
3376      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
3377    o pkg/autodiff/ctrl/grdchk :
3378      - attempt to sort out what works and what does not,
3379        with regard to I/O, and to warn/stop accordingly.
3380    o pkg/grdchk:
3381      - attempt to fix grdchk in the case of useSingleCpuIO.
3382      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
3383       statements were moved from grdchk_main.F and into
3384       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
3385      - a global sum is applied to record numbers icvrec/layer
3386       out of grdchk_loc so that they be passed to I/O routines.
3387    o pkg/smooth:
3388      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
3389        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
3390    o verification/testreport:
3391      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
3392      - can also use compressed (gzip) reference output file;
3393      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
3394        to be easier to collect by testreport.
3395      - update existing TLM output (half out-of-date by more than 3 yrs).
3396      - report NETCDF & LAPACK settings (from genmake2) in output dir.
3397      - report run-time in each individual summary (previously only for AD test);
3398        for TLM test, add also TAF version.
3399      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
3400    
3401    checkpoint63r (2012/08/15)
3402    o tools/genmake2:
3403      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
3404    o pkg/ecco/ecco_cost_final.F :
3405      - fix fc print statements (to stdout and costfunction0000) so
3406        that the printed value is always after the global sum.
3407    o pkg/seaice/seaice_dynsolver.F :
3408      - fix ice strength assymptote at SEAICE_area_max<1
3409        (no change for the standard case of SEAICE_area_max=1)
3410    o some cleaning:
3411      - pkg source files: ensure that all *.F files from each pkg included the
3412        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
3413        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
3414        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
3415        includes;
3416      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
3417      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
3418        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
3419        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
3420      - update option-file CPP_OPTIONS.h of all AD experiments:
3421        * no longer include PACKAGES_CONFIG.h ;
3422        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
3423        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
3424          including ECCO_CPPOPTIONS.h).
3425    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
3426      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
3427        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
3428        not necessary accurate).
3429      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
3430        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
3431        deliberately break compilation (a remainder that it needs to be customized)
3432      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
3433      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
3434      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
3435    o tools/genamke2:
3436      - check for lapack.
3437    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
3438      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
3439        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
3440        from both packages.
3441      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
3442      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
3443      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
3444        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
3445    o pkg/cost : add comments to explain special and/or untested setups.
3446    o pkg/exf:
3447      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
3448        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
3449    o verification/*/code_ad:
3450      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
3451      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
3452      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
3453        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
3454    o pkg/seaice :
3455      - added possibility to change ice strength/PRESS0 relationship to
3456        HEFF, according to the following run time parameters
3457        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
3458        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
3459        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
3460    o pkg/ggl90 :
3461      - added run time flag mxlSurfFlag to include the code that ensure
3462        mixing between first and second level (previously included as a comment)
3463    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
3464      - add test of newly added dumpAdByRec=T option where
3465        we write all records to one file per variable.
3466    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
3467      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
3468        to check that this code is ok with taf and compiles in adjoint.
3469    o pkg/autodiff :
3470      - added run time param dumpAdByRec : ad dump format switch.
3471        If true then write all records to one file per variable.
3472        Else write one file per record (remains the default).
3473      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
3474    o pkg/seaice:
3475     - Added SEAICEuseTILT run time switch : if set to
3476       false then omit the tilt term in seaice dynamics.
3477     - Fix free drift calculation.
3478    o pkg/shelfice:
3479      When initializing SHELFICEDragQuadratic, set default to be
3480      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
3481      but retain option to set it independently
3482      (inconsistenty spotted by Veronique Dansereau)
3483    o eesupp/inc:
3484      - in EEPARAMS.h, add real-type constant for some frequently used simple number
3485         (0,1,2,1/2), with name explicitly referring to RS/RL type.
3486    o model/src:
3487      - move balancing of relaxation terms to new S/R balance_relax.F.
3488    o pkg/autodiff:
3489      re-write active I/O high-level (control) S/R:
3490      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
3491      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
3492      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
3493        MDS_READ/WRITE_FIELD); change loops to multi-threads.
3494      - update and merge active_file_control_slice.flow into active_file_control.flow
3495      - update the calls in lower level S/R (active_file.F, active_file_g.F and
3496        active_file_ad.F) keeping the argument list and function unchanged.
3497      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
3498        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
3499      - new low-level active I/O routines, one for each type (RL/RS), for active var
3500        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
3501        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
3502        right type.
3503    o autodiff and RS=real*4:
3504      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
3505        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
3506      - change argument type of 3-D mask argument to _RS to match type in the call
3507        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
3508    o pkg/thsice:
3509      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
3510      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
3511        fresh-water flux: uniform correction or proportional to local precip.
3512    o pkg/ctrl:
3513      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
3514      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
3515                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
3516      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
3517    
3518    checkpoint63q (2012/07/30)
3519    o pkg/autodiff:
3520      note about monitor and snap-shot of ad-variables:
3521      a) need to apply ADEXCH before monitor or output of ad-vars to include
3522       overlap contributions (was done for adjDump but missing for monitor).
3523      b) since ADEXCH implies adding overlap values to interior array, machine
3524       truncation error is expected when adding an ADEXCH call in the middle of
3525       the time-stepping (although mathematically identical).
3526      modifs:
3527      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
3528        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
3529      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
3530        apply ADEXCH before monitor or snap-shot of ad-variables:
3531           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
3532      - implement new method (copy+adexch) for snap-shot and monitor of main model
3533        ad-vars (initially not used by default -> output unchanged).
3534      - change default (set to 2) to use new method and update few output_adm.txt
3535        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
3536        and both tutorial_tracer_adjsens tests).
3537      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
3538        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
3539    o pkg/ctrl:
3540      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
3541      generic control variables via
3542      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
3543      Only required customization should be S/R ctrl_map_ini_genarr.F
3544      (routine in repository contains example)
3545    o pkg/exf:
3546      - fix and refine checking of surface-relaxation setting when using EXF
3547    o verification (adjoint exp):
3548      - reduce length of simulation by half for experiment global_ocean.cs32x15
3549        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
3550    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
3551      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
3552        of KE that can occur with aggressive optimization
3553      + put quadratic bottom drag calculation in separated loops (only done if
3554        using bottomDragQuadratic)
3555    o model/src: CG2D_NSA
3556      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
3557         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
3558      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
3559         change cg2d residual target to be expressed in Wunits (=> do not normalise
3560         RHS ; this fix global_max Pb with TAF); update output.
3561    o verification/tutorial_tracer_adjsens:
3562       improve parameter consistency (and get rid of warnings):
3563       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
3564       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
3565       - use staggerTimeStep (for stability) in som81; use default rotation period.
3566    o pkg/exch2:
3567      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
3568        reset to 0 = 1 long line in X)
3569    o pkg/mdsio:
3570      - fix reading of dimensions from meta file for large-size domain
3571    o model/src:
3572      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
3573      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
3574        Cubed-Sphere Exch with CS-corners inside the domain;
3575        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
3576        globalArea and to set hasWetCSCorners.
3577      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
3578        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
3579      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
3580        useCDscheme and useCubedSphereExchange).
3581    o pkg/seaice/seaice_growth.F :
3582      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
3583        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
3584        when the previous code was not correct.
3585      - in all cases diagnoze the boundary condition mismatch to SIaaflux
3586      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
3587        that term to QNET (essentially to set the melt/freeze water to 0degC).
3588        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
3589    o verification/global_ocean.cs32x15/input.seaice :
3590      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
3591      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
3592      - update results (output.seaice.txt) accordingly.
3593    o verification/lab_sea/input/data.seaice :
3594      - remove SEAICEheatConsFix, which is now be tested
3595        in global_ocean.cs32x15. The presently coded fix
3596        is only consistent with real fresh water + nlfs.
3597      - update results (output.txt) accordingly.
3598    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
3599    o AD_CONFIG.h file:
3600      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
3601      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
3602        add it explicitly in each fortran src file where it is needed.
3603        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
3604        thus introducing potentially wrong dependency; therefore, better to include
3605        it only where it's really needed, and after any other included OPTIONS file
3606        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
3607        or ALLOW_TANGENTLINEAR_RUN).
3608    
3609    checkpoint63p (2012/07/06)
3610    o pkg/autodiff:
3611      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
3612      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
3613        which are now read from new parameter file "data.autodiff" (inAdExact
3614        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
3615      - add file "data.autodiff" in all verification/*/input_ad/ directories.
3616      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
3617        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
3618    o verification/tutorial_tracer_adjsens/
3619      - add extra sub-verification which uses "SOM" advection scheme
3620        (2nd Order-Moment Advection Scheme, Prather Limiter) with
3621          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
3622        and in data:
3623          multiDimAdvection=.TRUE.,
3624          tempAdvScheme=81,
3625          saltAdvScheme=81,
3626    o model/src:
3627      - introduce ALLOW_BALANCE_RELAX which allow the removal
3628       of the global mean of relaxation terms by setting
3629       balanceThetaClimRelax and balanceSaltClimRelax
3630      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
3631       This case is now treated appropriately in seaice_growth.F
3632    o pkg/seaice:
3633      - do balanceEmPmR and balanceQnet based on the net fluxes
3634        (SItflux) that enter the ocean+ice system rather than QNET
3635        and EMPMR. Works best in real fresh water.
3636      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
3637        out of the diagnotics bloc, and stored in global arrays.
3638    
3639    checkpoint63o (2012/06/29)
3640    o vertical mixing schemes:
3641      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
3642      - replace computation of density (in Function STATE1, opps_calc.F) by a call
3643        to S/R FIND_RHO_SCALAR
3644      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
3645        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
3646        affects output (vermix.ggl90) at truncation level.
3647    o testreport:
3648      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
3649        (nSx,nSy) for the number of threads (from eedata.mth)
3650    o model/src:
3651      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
3652        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
3653    o verification/tutorial_tracer_adjsens/
3654      - compile with ALLOW_CG2D_NSA
3655      - run with nonlinFreeSurf=3
3656      - update reference output_adm.txt
3657    o tools/genmake2:
3658      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
3659        refine usePROFILES switching off (only when NetCDF is not available).
3660    o verification (atmospheric set-up):
3661      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
3662    o pkg/profiles : refine profiles and files handling.
3663    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
3664    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
3665      - changes to use model/src/the_main_loop.F rather than the ecco version
3666        in ecco type adjoint runs.
3667    o model/src:
3668      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
3669      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
3670      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
3671    o model/src:
3672      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
3673        update output of test experiment bottom_ctrl_5x5.
3674    o pkg/generic_advdiff:
3675      - implement vertical bi-harmonic diffusion (for now, only for T & S and
3676        only explicitly).
3677    o verification/bottom_ctrl_5x5/
3678      update reference output (results changed quite some time ago,
3679      not sure when; but new reference results look ok in terms of grdchk)
3680    o verification/1D_ocean_ice_column/
3681      For verification purposes, the exact adjoint rather than an approx.
3682      should be used (e.g., to comare against F.D. or TLM).
3683      removed autodiff_inadmode*_ad.F routines in code_ad/
3684      Update results/ accordingly.
3685    o pkg/cal:
3686      - change cal_getdate.F so that output date is function of input time only
3687        (less ambiguous, not mixed up with input iteration number).
3688      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
3689    o pkg/diagnostics:
3690      - implement calendarDumps also for stats-diags
3691      - implement calendarDumps also for snap-shot output (negative freq)
3692      - for now, ignores calendarDumps if non-zero phase-lag.
3693    
3694    checkpoint63n (2012/06/04)
3695    o model/src:
3696      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
3697        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
3698      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
3699        similar to calc_r_star.F); update results of experiment internal_wave and
3700        tutorial_global_oce_in_p (affected @ truncation level).
3701    o pkg/shelfice:
3702      - add parameterisation of advective-diffusive flux into the ice shelf
3703        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
3704      - simply eps3/3a computation
3705    o eesupp:
3706     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
3707       between tiles, just fill-in edges assuming locally periodic subdomain) and
3708       add corresponding exchange subroutines (EXCH0);
3709     - new CG-solver version (_EX0) for disconnected-tiles special case.
3710    o model/src (CG-solvers):
3711     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
3712       (similar final residual output and max-Iter number as with standard version);
3713     - allows to store and use lowest-residual solution (standard & _SR versions);
3714     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
3715     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
3716    o eesup/src:
3717     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
3718       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
3719    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
3720    
3721    checkpoint63m (2012/04/27)
3722    o pkg/shelfice:
3723     - account for partical cells in surface level below ice-shelf for hydrostatic
3724       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
3725    o ad test experiments:
3726     - update and rename to "ad_optfile.local" local AD-optfile specific to a
3727       particular adjoint verification experiment (in verification/*/code_ad/)
3728    o pkg/seaice & pkg/exf:
3729     - Part two of ECCO-CLIVAR code merges.
3730       Completes merge of seaice area relax. code.
3731       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
3732       to be set in EXF_OPTIONS.h since this pkg controls its I/O
3733       (and avoids second CPP option in SEAICE_OPTIONS.h)
3734     - change default value of costIceStart & costIceEnd to a valid date.
3735     - add snowPrecip to HSNOW in seaice_growth
3736    o pkg/ptracers:
3737     - move ptracers summary and setup check into separated S/R ; add a check for
3738       valid PTRACERS_Iter0 value (error+stop or just warning).
3739    o pkg/cal (+ pkg/ecco):
3740     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
3741       as input; and for AD, unless both are not differentiable (e.g., k index)).
3742    o model/src:
3743     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
3744       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
3745       temporary set to usingZCoords value (to be changed to F when using shelfice).
3746     - hydrostatic pressure: implement partial cell near the surface also for
3747       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
3748       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
3749    o pkg/ctrl/ctrl_init.F:
3750     - add a formal parameter to s/r ctrl_init_rec to print
3751       xx_$(ctrl_valiable)_file for easier debugging
3752     - move call of cal_* routines into the if-block where they are really
3753       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
3754       to specify a startdate
3755    o pkg/seaice:
3756     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
3757       global_ocean.cs32x15/code versions).
3758     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
3759       verification experiment global_ocean.cs32x15.seaice and update results.
3760    o pkg/exf:
3761     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
3762       (according to useExfYearlyFields).
3763    o pkg/cal:
3764     - move calendar setting & summary (previously in cal_readparams.F) into new
3765       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
3766       length of the simulation is set (after SET_PARMS call); This is an attempt
3767       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
3768     - For safety: keep a record of pkg/cal parameter settings status
3769               to allow to STOP if one pkg/cal S/R is called too early.
3770     - add a stop in all basic pkg/cal subroutines if called before setting is done.
3771     - modify cal_getdate.F: stop when nothing was returned;
3772       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
3773       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
3774    
3775    checkpoint63l (2012/04/04)
3776    o pkg/bbl:
3777      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
3778        update global_with_exf output.yearly.txt file.
3779    o pkg/cal:
3780      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
3781      - remove 2 unsused and very short (1 line only) functions ;
3782      - remove unsused subroutines from AD-Diff list.
3783    o model/src:
3784      - start to implement clean wait to stop in initialization S/R (config_check.F,
3785         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
3786    o folowing PRINT_MESSAGE changes:
3787      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
3788    o pkg/bbl:
3789      - modification so it can work with z*
3790      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
3791      - global_with_exf/input.yearly verification; changes output.yearly.txt
3792    o eesupp/src:
3793      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
3794        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
3795      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
3796        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
3797      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
3798      - when using MPI, always set usingMPI=T ; set default accordingly and stop
3799        if not consistent.
3800      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
3801        argument is zero (in case called within single-thread section).
3802    o pkg/fizhi:
3803        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
3804        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
3805    o pkg/exch2:
3806      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
3807        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
3808      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
3809        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
3810        with bad ones coming from a not-yet-updated halo.
3811        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
3812    o pkg/frazil:
3813        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
3814        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
3815    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
3816    o verification/lab_sea
3817      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
3818      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
3819      * nTimeSteps 3 -> 4
3820      * changed reference output accordingly
3821    o pkg/ctrl:
3822      * fix ctrl_get_gen for xx_sst, xx_sss
3823    o pkg/fizhi:
3824      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
3825        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
3826      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
3827        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
3828        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
3829    o pkg/gmredi:
3830      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
3831    o pkg/fizhi:
3832      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
3833        (old)aces open64 tuv test.
3834    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
3835    o pkg/mom_vecinv:
3836      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
3837        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
3838        with non-lin free-surf).
3839    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
3840      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
3841      some compilers (gfortran 4.6.0 on MacOS)
3842    o momentum:
3843      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
3844        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
3845        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
3846    
3847    checkpoint63k (2012/03/17)
3848    o model/src:
3849       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
3850         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
3851       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
3852         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
3853    o model/src: solve_*diagonal.F
3854       - replace division with multiplication by inverse (similar to original version)
3855         update output of AD exp. global_ocean.90x40x15.
3856       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
3857         to enable the use of the vectorized & differentiable solve_tridiagonal.F
3858       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
3859         vertical advection (to get solve_tridiagonal tested in AD mode).
3860    o pkg/seaice: ECCO-CLIVAR merge:
3861      1. seaice AREA relaxation
3862         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
3863         * runtime flag: SEAICE_tauAreaObsRelax
3864      2. modified global mean cost imbalance code: CPP option
3865          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
3866    o another iteration on solve_*diagonal.F
3867       Make choices independent of AUTODIFF
3868       Default will be the adjoinable vectorized version.
3869       Alternative choices are:
3870       * non-adjoinable original version with low memory footprint:
3871         #define SOLVE_DIAGONAL_LOWMEMORY
3872       * still adjoinable but does not vectorize (k as inner-most loop):
3873         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
3874    o testreport
3875     - add option to use a home made wrapper around "make"
3876     - remove MITGCM_IEEE env. variable (no longer active)
3877    o pkg/shelfice
3878     - improve computation of friction velocity for velocity dependent
3879       exchange coefficients: include velocities into SHELFICEBoundaryLayer
3880       block to average velocities vertically
3881     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
3882    o Modify diagonal solvers, now three versions (upon request):
3883      #ifndef SOLVE_DIAGONAL_AUTODIFF
3884        1. default version (dating back a while ago)
3885      #else /* def SOLVE_DIAGONAL_AUTODIFF */
3886      # ifdef SOLVE_DIAGONAL_KINNER
3887        2. adjoinable version with k-innermost loop (G. Forget)
3888      # else
3889        3. adjoinable vectorized version of 2.
3890      # endif
3891      #endif /* SOLVE_DIAGONAL_AUTODIFF */
3892      All flags are currently set within routines, but could/should be moved to CPP-options.
3893      Array bounds for 1. are as before, for 2.,3. cover the entire domain
3894      (could be changed for 1. too).
3895    o verification/lab_sea (fwd):
3896      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
3897        use 7 categories (except hb87), new solve4temp params (except salt_plume),
3898        constant salinity (=4) or variable salinity (salt_plume) done through
3899        SItracer.
3900    o pkg/seaice:
3901      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
3902      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
3903         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
3904        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
3905        SEAICE_freeze got retired) but already better than previously with
3906        SEAICE_freeze=123456.7 deg.C;
3907      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
3908        (safer multi-threaded setting); always set SEAICEuseEVP;
3909      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
3910        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
3911        stop if multiple specifications for the same coeff; make sure default
3912        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
3913    o pkg/obcs:
3914      - allow to switch to upwind 1rst order advection scheme for the advective
3915        flux computation at the open-boundary; disabled for adjoint built.
3916    o pkg/ptracers:
3917      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
3918      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
3919      - add parameter to decide when to start a tracer; use internal flag to
3920        know which tracer to step-forward; switch this internal flag at the top
3921        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
3922        for adjoint built.
3923    o pkg/seaice:
3924      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
3925      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
3926      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
3927    o pkg/ecco:
3928      - fix writing of output file DiagnosCost_ClimSalt/Theta
3929        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
3930    o pkg/seaice:
3931      - add missing initialisation of COR_ICE array in dynsolver.F
3932      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
3933        compiled either way, and is tested in all exps (multidim was only tested
3934        in lab_sea ad before).
3935      - cosmetic change to prepare for future addition of ITD. no change to results.
3936        no defaults change.
3937      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
3938      - by lack of adequate verification experiments, I further used custom versions
3939        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
3940        should be correct.
3941      - avoid recomputations in ad.
3942    o array initialisation in adjoint mode:
3943      1) pkg/mom_common/mom_calc_ke.F:
3944        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
3945        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
3946        part this initialisation is gone, resulting in Floating Point Exception
3947        (caught by open64 compiler with debug option).
3948      2) model/src/convective_weights.F
3949        set output convectCount over the full array range (instead of doing
3950        an update): this fix a similar issue when called within recomputation (adjoint)
3951        which could by-pass the initialisation (normally done in the caller S/R).
3952    o pkg/seaice:
3953      - final version of turbulent flux params, as agreed at MIT ice meet:
3954           SEAICE_mcPheePiston (default is ~ 0.000875)
3955           SEAICE_mcPheeTaper (default is 0.)
3956           SEAICE_frazilFrac (defualt is 1.)
3957           SEAICE_mcPheeStepFunc (default is false)
3958      - changes results at trunction error level
3959      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
3960    o added pkg/frazil:
3961      - see frazil_description.tex for details
3962      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
3963    o pkg/shelfice/shelfice_thermodynamics.F
3964      - fix exponents for velocity dependent exchange coefficients: change
3965        from 2/3(=0) to 0.66666666666666667
3966      - move computation of velocity dependent exchange coefficients into
3967        separate loop, so that it applies to both thermodynamics
3968      - move some divisions by constants out of loops
3969    
3970    checkpoint63j (2012/02/16)
3971    o pkg/seaice:
3972      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
3973      - SItracer:  added run time params, and allow coupling to ocn salinity.
3974    o pkg/seaice: remove (almost) all divisions by constants within loops
3975      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
3976      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
3977      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
3978      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
3979    o pkg/seaice :
3980      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
3981        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
3982      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
3983      - add permanent SItflux diag that corresponds to TFLUX but includes
3984        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
3985      - allow activation/testing of a fix for suspected missing term in
3986        ocn-ice heat budget (to be confirmed). To test this, you want to
3987        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
3988        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
3989      - no change in results, fwd or ad.
3990    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
3991      - switch to variable freezing point.
3992           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
3993      - bug fix : the sublimation term that was missing is now activated.
3994           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
3995      - bug fix : flooding sign term for SIsal0.NE.0.
3996           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
3997    o pkg/seaice:
3998      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
3999        is now the default, and the old default constant freezing point is recovered
4000        with SEAICE_tempFrz0    = -1.96,
4001             SEAICE_dTempFrz_dS = 0.,
4002      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
4003      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
4004      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
4005        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
4006      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
4007        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
4008      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
4009        seaice_growth r149 for legacy branch (no results change).
4010      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
4011        from I. Fenty).
4012      - results did not change except for global_ocean.cs32x15, mostly due to the
4013        switch to variable freezing point (see above item for detail).
4014    o pkg/thsice:
4015      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
4016        seawater freezing in thsice_calc_thickn (not used).
4017    o pkg/seaice: turbulent flux term specification via run time params.
4018      - replace CPP switches with run time switches to facilitate testing
4019      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
4020                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
4021      - added runtime parameter : SEAICEturbFluxFormula
4022      - move Mcphee constants to SEAICE_PARAMS.h
4023      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
4024                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
4025                 remove seaice_summary call (moved to seaice_init_fixed)
4026      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
4027        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
4028      - seaice_summary.F : add missing report of read turbulent flux term set up
4029                           and SITRACER.
4030      - seaice_check.F : check range; inform and stop if retired CPPs are used
4031                         (incl. SEAICE_AGE).
4032      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
4033             CPP switch, same computation as before for the different options.
4034      - change results at the truncation level.
4035    o pkg/seaice:
4036      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
4037        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
4038        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
4039      - update verification/*/input*/data.seaice:
4040        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
4041        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
4042        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
4043        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
4044    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
4045      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
4046        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
4047        difference in results only due to machine truncation.
4048      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
4049        MaykutPolySatVap; keep MIN_LWDOWN.
4050      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
4051      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
4052        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
4053    o pkg/salt_plume:
4054      - isolate saltPlumeFlux array exch into a specific S/R called from
4055        do_oceanic_phys.F
4056      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
4057    o verification:
4058      - move untested set-up to MITgcm_contrib/verification_other.
4059    o pkg/seaice:
4060      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
4061    o pkg/seaice:
4062      - seaice_solve4temp.F (keeping results unchanged):
4063        * add 2 future run-time params to select which saturation vapor pressure
4064          formula is used and how post-iteration fluxes are set.
4065          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
4066        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
4067          the linearized expression to stay consistent with tsurf finding.
4068      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
4069        can be < 0.
4070    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
4071      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
4072        conductive heat flux F_c , and add it explicitly when updating tsurf as
4073        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
4074        so that now F_ia has a consistent meaning through the entire routine.
4075        This causes differences at truncation level: update output of fwd exp.
4076        global_ocean.cs32x15.seaice.
4077    o pkg/seaice:
4078      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
4079        of arrays, sign/direction of fluxes; no effect on results.
4080      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
4081        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
4082        note: this should have been done before changing celsius2K default.
4083      - to keep results unchanged, add back old value of celsius2K in verification
4084        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
4085      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
4086        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
4087        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
4088        freezing temp is consistent with value in seaice_growth.F ; this causes
4089        differences at machine truncation level: update lab_sea AD output (3/4).
4090    o pkg/seaice:
4091      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
4092        and climsst/sss even when using seaice (to prevent calculation that might
4093        use SST on land); does not affect any verification exp.
4094      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
4095        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
4096    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
4097      over land (non-legacy code)
4098    o vectorize salt_plume package:
4099      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
4100      - this code computes plumebk everywhere (also over land), thus requires
4101        code to avoid divisions by zero and catch the case of kLev=Nr.
4102      - efficiency of salt_plume_frac is still sub-optimal
4103    o tools (genmake2):
4104      - fix makefile NAME specification (option: -makefile NAME) by adding
4105        "-f $MAKEFILE" in few places where it was missing including makedepend
4106        command (contribution from Paul).
4107    
4108    checkpoint63i (2012/01/24)
4109    o model/src:
4110      - add factorized versions of some EOS code to find_rho.F,
4111        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
4112    o model/src:
4113      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
4114      - change default celsius2K from 273.16 to 273.15
4115      - to keep results unchanged, add back old value of celsius2K in verification
4116        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
4117         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
4118    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
4119      to make TAF generate vectorizable code
4120    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
4121       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
4122       have flags that do this more efficiently.
4123    o pkg/diagnostics/diagstats_calc.F
4124      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
4125    o pkg/obcs (with exch2):
4126      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
4127        and remove code (in obcs_readparms.F) which was based on EXCH of indices
4128        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
4129    o pkg/exf and seaice exp:
4130      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
4131        so that switching off area & heff advection flags does not affect results.
4132      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
4133      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
4134        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
4135        results of verification experiments: 1D_ocean_ice_column(fwd),
4136        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
4137        and offline_exf_seaice (all 4).
4138    o pkg/seaice:
4139      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
4140        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
4141      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
4142        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
4143        not multi-dim advection;
4144      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
4145        SHORTWAVE_HEATING #undef.
4146    o optim: make Makefile more robust (?)
4147    o pkg/obcs:
4148      * fix treatment of obcs_read_pickup for TAF
4149    o pkg/shelfice:
4150      * add missing initialisation of num_shifwflx
4151      * new adjoint verification exp. for isomip
4152      * change Prandtl and Schmidt numbers from generic formulations
4153        (in terms of model diffus. and visc.) to separate runtime
4154        parameters, with Holland and Jenkins (1999) default values.
4155    o pkg/exf (interpolation):
4156      - extended input field (2 rows) near the N & S poles:
4157        * fill in with the symetric value (when even Nb of data in longitude)
4158        * add average value at the poles only for scalar quantities ; for vector
4159          component interpolation, skip the averaging and keep duplicated values,
4160          unless the 2 components have same location (uvInterp=T) in which case
4161          interpolate the 2 components together using S/R EXF_INTERP_UV.
4162      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
4163        together: this allows to account properly for local orientation when
4164        averaging at N & S pole.
4165      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
4166        exf-interpolation near N & S poles. Undef by default.
4167      - add debug check/print on 1rst iter if debugLevel >=2.
4168    o pkg/exf:
4169      - change masking flags definition (no longer "parameter"), put them in
4170        common block and set them in S/R EXF_INIT_FIXED.
4171      - change recognized masking flag from s,u,v to c,w,s since the mask
4172        to use (maskC,W,S) depends on position on model grid and has little to
4173        do with scalar/vector difference; fix masking if using P-coordinates.
4174      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
4175        and update results of exp. global_with_exf (x2).
4176      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
4177    o pkg/obcs
4178      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
4179    o pkg/exf (interpolation):
4180      - assume periodicity in X only if input field cover full longitude range.
4181      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
4182        and should vectorise).
4183      - fix input lat of the 2 added row (in case we provide N.pole data).
4184    
4185    checkpoint63h (2011/12/30)
4186    o pkg/seaice:
4187      - change declaration of UVM from _RL to _RS in order to get B-grid
4188        uIce,vIce monitor when _RS = real*4
4189    o pkg/offline:
4190      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
4191      - compute vertical velocity if not read from file (switch on exactConserv
4192        & staggerTimeStep);
4193      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
4194    o verification:
4195      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
4196        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
4197        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
4198      - update output of exp. global_ocean.cs32x15.viscA4 after changing
4199        grid-file angles (used here for coriolis-3d);
4200      - remove (or gzip) few files not needed to run fizhi-cs experiments.
4201    o pkg/exf (vector interpolation):
4202      - rotate vector component toward local grid-axis orientation using grid-angles
4203        (stored in GRID.h) instead of locally computed rotation angle; keep old code
4204        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
4205    o pkg/seaice:
4206      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
4207        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
4208    o pkg/PKG_OPTIONS.h files:
4209      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
4210        outside of the #ifdef ALLOW_THISPKG / #endif block.
4211      - update verification/*/code/PKG_OPTIONS.h files.
4212    o add a verification experiment (offline_exf_seaice/input.seaice) that test
4213      the B-grid LSOR solver
4214    o pkg/seaice: sort out emissivity and long wave radiation step 2:
4215      - add emissivity for snow and ice as new run-time parameters
4216        (unfortunately) that default to the corresponding exf values; this
4217        changes results in most verification experiments so that for backward
4218        compatibility these parameter have to be set explicitly to inconsistent
4219        values (ugly);
4220      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
4221        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
4222        until we agree how to handle this bug properly
4223    o pkg/exf (interpolation):
4224      - add a set of run-time param ({inputfield}_interpMethod), one for
4225        each interpolated input field, to select the interpolation method
4226        with a value of zero switching off the interpolation;
4227      - print interpolation parameters to standard output;
4228      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
4229        (to use instead runoff_interpMethod=0 in data.exf).
4230      - simplify default setting of interpolation parameters (for all fields,
4231        set position to match model grid cell-center position, leading to trivial
4232        interpolation in case of regular Lat-Lon grid) and fix for the case of
4233        non-uniform delY.
4234    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
4235       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
4236       this factor is absolutely required, because the lw exitance (= out-going
4237       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
4238       where the reflectivity rho = 1-emissivity for conservation reasons. Once
4239       this is established, we can remove the CPP-Flag (if we want to).
4240    o pkg/seaice:
4241      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
4242        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
4243      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
4244        what the name implies (and not emissivity*BoltzmannConstant), this means
4245        the old default value of 5.5e-8 now means
4246        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
4247        S/R exf_readparms
4248      - FV-discretization of the B-grid LSOR solver, turn on with
4249        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
4250        of the calling routine dynsolver, so that B and C-grid code look a
4251        little more alike.
4252      - fix index bugs in ostres.F (B-grid code)
4253    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
4254    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
4255      default for SEAICE_emissivity, if useEXF; requires setting a wrong
4256      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
4257      backward compatiblity
4258    o model/src: use sigmaR in calc_ivdc
4259    
4260    checkpoint63g (2011/12/16)
4261    o pkg/seaice/seaice_growth.F:
4262      fix heat conservation of the coupled ocean-seaice system.
4263      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
4264      solid vs liquid water treatment is resolved via QNET.
4265    o pkg/seaice/seaice_growth.F:
4266      add missing term for sublimation in saltFlux, which was breaking conservation.
4267    o pkg/seaice/seaice_model.F:
4268      Remove this patholigical case treatment in evolution branch,
4269      where it is un-necessary and breaks conservation.
4270      Update global_ocean.cs32x15/results accordingly for
4271      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
4272    o model/src:
4273      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
4274      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
4275    o pkg/obcs:
4276      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
4277      tendency for temperature and salinity that is then applied to update
4278      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
4279      horizontal advection and diffusion contributions on the boundary (in
4280      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
4281      removing the mask in S/R timestep_tracer. The advantage of this approach is
4282      that the updated tracer values include contributions from the surface
4283      forcing and vertical diffusion.
4284      This modification changes exp4.stevens because of vertical diffusion.
4285    o model/src:
4286      change non-curvilinear grid setting to also work with exch2 + blank tiles:
4287      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
4288        face dimensions.
4289      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
4290        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
4291        and INI_SPHERICAL_POLAR_GRID.
4292      change test-experiment global_ocean.90x40x15:
4293      - split the domain in many more tiles (9x4 tiles of 10x10 each);
4294      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
4295      - update results of both test (std & dwnslp).
4296    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
4297       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
4298    o model/src:
4299      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
4300        and fix initialisation when using sigma-coords.
4301    o model/src:
4302     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
4303       to their current value at the beginning of forward_step.F": add a new run-time
4304       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
4305     - set doResetHFactors=T in the following test exp:
4306        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
4307        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
4308        and tutorial_global_oce_in_p (nonLinFS in p)
4309    o pkg/ecco
4310      - added IES cost term
4311    o verification/advect_xz
4312      - scale down the depth by 1/100 (from 200 km to just 2.km)
4313      - add secondary test using divergent flow, r-star and implicit vertical advection.
4314      - add note (check_conserve_TS.txt) and matlab script to check global
4315        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
4316    o pkg/rbcs:
4317      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
4318    o pkg/obcs (Stevens BCs):
4319      - fix various problems in the phase speed computations of the Stevens
4320        boundary conditions:
4321        - sign error for western and southern boundaries,
4322        - time tendencies were underestimated by factor of dTracerLev and some just
4323          zero (for multidim advection schemes) -> now estimate time tendencies
4324          from difference between previous (n) time level and the one before (n-1);
4325          this requires storing a field per tracer per boundary, also in the pickup
4326          files.
4327        - replace deltaTmom in cflMer/Zon computation with dTracerLev
4328        - set default phase velocity to cflMer/Zon
4329      - update verification experiment exp4.stevens
4330    o pkg/generic_advdiff (implicit_r):
4331      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
4332        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
4333      - fix implicit vertical diffusion or advection with NonLin FreeSurf
4334        (was using current recip_hFacC instead of future recip_hFacC): set future
4335        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
4336        solver S/R ;
4337      - fill diagnostics of vertical advective fluxes (computed from tendency)
4338        when using implicit vert. advection;
4339      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
4340         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
4341         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
4342         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
4343    o pkg/diagnostics:
4344      - add diags for T & S tendency which goes through Adams-Bashforth.
4345    
4346    checkpoint63f (2011/11/30)
4347    o pkg/obcs/obcs_calc_stevens.F:
4348      - join some loops to reduce number of if-statements
4349      - fix a bug in code for northern and southern boundaries.
4350    o pkg/seaice/seaice_init_varia.F
4351      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
4352        caused zero ice-velocities for the B-grid code
4353    o pkg/seaice/seaice_init_fixed.F
4354      - fix a bug in the initialisation of the second metric terms
4355        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
4356      - this affects all seaice configurations with useCurviLinearGrid = .true.
4357        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
4358        = .true. (default)
4359      - the only verification experiment affected is global_ocean.cs32x15:
4360        icedyn, seaice, and seaice_dynmix (AD)
4361    o pkg/thsice/thsice_diagnostics_state.F
4362      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
4363        not contain garbage that can lead to surprises in diagstats_calc.F
4364    o model/src:
4365      - move bi,bj loops inside INTEGR_CONTINUITY ;
4366      - call INTEGR_CONTINUITY directly from forward_step.F
4367        (previously called from momentum_correction_step.F)
4368      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
4369        forward_step.F and pkg/ecco/the_main_loop.F
4370    o model/src/do_oceanic_phys.F:
4371      - reset addMass to zero only if useICEFRONT ;
4372      - separated k-loop for rhoInSitu calculation ;
4373      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
4374        and at constant T,S (= WdRHOdP);
4375      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
4376        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
4377        transport of locally-referenced potential density);
4378        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
4379    o gluemnc:
4380      - replace ncrcat with ncks when adding variables to *.glob.nc
4381      - change the way variables without record dimensions are handled so that
4382        files that have variables with and without record variables can be glued:
4383        add a record dimension with a new unique name to be able to differentiate
4384        between variable with and without a-prior record dimensions. Remove
4385        this record dimension before adding the variable to the *.glob.nc file.
4386        This procedure automatically works also for grid.*.nc files that do not
4387        have any record dimension.
4388    o verification/cpl_aim+ocn:
4389      - generate new reference output on baudelaire (gfortran, mpich2) (previously
4390        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
4391    o pkg/obcs/obcs_calc_stevens.F:
4392      - add code for northern and southern boundaries.
4393      - reorder some loops to save some operations and so that drFBar can be scalar
4394    o model/src:
4395      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
4396        truncation) and add diagnostics for Adams-Bashforth tendency increment.
4397      - update test-exp. AD output:
4398        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
4399      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
4400        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
4401        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
4402        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
4403        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
4404        tutorial_plume_on_slope.
4405    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
4406      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
4407      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
4408      does not even come with an F77 compiler anymore, this should not be
4409      a limitation
4410    
4411    checkpoint63e (2011/11/06)
4412    o pkg/seaice adjoint of LSR:
4413      - substantially rework STORE dirs.
4414      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
4415        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
4416        and only perform SOLV_MAX_FIXED adjoint iters.
4417        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
4418        always goes to same record, meaning that the last forward field will be
4419        the one used in the adjoint - an approximation.
4420      - now produces non-zero LSR-related gradients, and acceptable gradients for
4421        An's zonal (x-z) test case (to be checked in)
4422      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
4423        (but these are screwed up by the thermodynamics in the first place);
4424        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
4425        output_adm.txt also reflects changes to seaice_lsr
4426      - global_ocean.cs32x15:
4427        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
4428          (output_adm.seaice.txt was updated)
4429        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
4430          (output_adm.seaice_dynmix.txt)
4431    o test-exp. exp4+stevens:
4432      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
4433    o pkg/seaice (lsr solver):
4434      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
4435        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
4436      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
4437      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
4438        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
4439      - compute (with new S/R) and print initial (+ free-driff sol. if available)
4440        and final residual of linearised system.
4441    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
4442      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
4443    o pkg/obcs: Stevens BCs (still only for east and west)
4444      - fix Stevens BCs by using intermediate velocities of previous
4445        time step as "baroclinic" contribution rather velocity of one grid cell
4446        inside the boundaries; more consistent but makes the entire treatment
4447        more complicated, requires new pickup files and two new S/Rs:
4448        obcs_copy_uv_n and obcs_save_uv_n
4449        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
4450        (undefined by default)
4451      - silently move computation of some grid factors into separate loops to
4452        save some recomputations
4453      - add a hack for non-linear free surface
4454      - add a verification experiment to exp4 that tests this code
4455    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
4456    
4457    checkpoint63d (2011/10/25)
4458    o pkg/obcs + seaice-dynamics:
4459      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
4460        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
4461        values (consistent with an implicit method).
4462      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
4463        return to older implementation (same results as before); note that none of
4464        the "experimental" OBCS_SEAICE options are implemented in the new version.
4465      - switch test exp. seaice_obcs to use new version (update output).
4466    o pkg/seaice:
4467      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
4468      - add parenthesis in Water-Ice drag calculations (evp & lsr);
4469      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
4470        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
4471      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
4472        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
4473    o pkg/layers:
4474      - Include potential density as new coordinate (Thanks to David Munday)
4475    o pkg/dic:
4476      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
4477        carbonate computation/output to CALC_PCO2_APPROX
4478    o pkg/generic_advdiff
4479      - make TAF generate code that vectorizes:
4480        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
4481    o model/src:
4482      - improve vectorization also for adjoint code of
4483        solve_tridiagonal and solve_pentadiagonal. As this requires up to
4484        5 new 3D-fields, this code is only turned on for the combination of
4485        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
4486        for singular matrix check (only for TARGET_NEC_SX).
4487      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
4488        ALLOW_AUTODIFF. This flag now needs to be set outside of
4489        solve_tri/pentadiagonal.F
4490    o pkg/exf:
4491      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
4492        optional namelist EXF_NML_OBCS).
4493      - add many debug-print (to trace down where pkg/cal error msg comes from)
4494    o pkg/mom_vecinv/mom_vi_hdissip.F
4495      - rearrange loops so that vectorization is improved and in particular
4496        the adjoint routine vectorizes. The code is a little longer now, but I
4497        think easier to read.
4498        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
4499    o pkg/seaice:
4500      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
4501    o pkg/exch2:
4502      - alternative code (without tile x tile matrix) for cumulated (global) sum;
4503        used as default; keep using matrix version in adjustment.cs-32x32x1.
4504    o tools/build_options:
4505      - after merging some MPI and/or multi-threads specific optfiles so that
4506        the modified default optfile support both built (using genmake2 -mpi
4507        for the MPI built, using genmake2 -omp for OpenMP built),
4508        move now obsolete optfiles to tools/build_options/unsupported/
4509       (add copy of email sent to support list in doc/optfiles_changes.txt)
4510    
4511    checkpoint63c (2011/09/28)
4512    o pkg/ebm:
4513      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
4514        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
4515    o pkg/seaice (SItracer pickup)
4516    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
4517      To be done:
4518      - thorough testing of missing fields in S/R seaice_read_pickup
4519      - thorough matching between generic tracers and specific fields used
4520        (e.g. volume-weighted age, area-weighted age, salinity, ...)
4521    o pkg/grdchk:
4522      - all procs calculate and print finite-difference gradient (for testreport)
4523      - change description output used by testreport;
4524      - AD testing: also compare and report Finite-difference gradient;
4525        => update all output_adm*.txt
4526    o test exp. global_ocean_ebm:
4527      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
4528        and turn on exactConserve; update (fwd) output.
4529    o pkg/seaice (LSR):
4530      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
4531      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
4532        * identical results with non-CS topology (but save up to half of EXCH calls)
4533        * no much changes in cs-32 verification tests since no ice at face edges
4534         (differences due to convergence criteria, since nb of iterations changed)
4535        * expect some differences on lat-lon-cap grid.
4536        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
4537    o pkg/exch2:
4538      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
4539        many tiles); until alternative coding is added, just add a stop.
4540    o pkg/kpp:
4541      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
4542        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
4543    o optfiles:
4544      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
4545        into corresponding standard one, which now support different build:
4546        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
4547      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
4548    o pkg/obcs (seaice):
4549      - add missing EXCH for uIce,vIce after applying OBCS;
4550      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
4551        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
4552        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
4553      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
4554      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
4555        and eedata.mth for MPI and mutlti-threaded testing.
4556    o pkg/flt:
4557      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
4558      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
4559      - fix pickup and trajectories + profiles output with multi-threads;
4560      - add parameter to select group of fields to write along trajectory and
4561        profile (default unchanged);
4562      - only call PORT_RAND* function when flt_noise <> 0;
4563      - add multi-threaded test for verification exp. flt_example.
4564    o eesupp/src:
4565      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
4566      - USE_OMP_THREADING: check that number of threads (from eedata) matches
4567        actual number (from env.var. setting).
4568    o pkg/ebm:
4569      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
4570      - add multi-threaded test for verification exp. global_ocean_ebm
4571    
4572    checkpoint63b (2011/08/29)
4573    o pkg/ebm:
4574      - fix sign of runoff;
4575      - update directly forcing fields (Qnet,EmPmR) to use standard
4576        external_forcing_surf.F (remove ebm_forcing_surf.F);
4577      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
4578      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
4579        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
4580      - update global_ocean_ebm parameters file data and update output (fwd+ad).
4581    o verification/matrix_example:
4582      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
4583        MPI and mutlti-threaded testing.
4584    o pkg/matrix:
4585      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
4586      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
4587      - fix for multi-threaded (remove DATA statement);
4588      - use standard DIFFERENT_MULTIPLE function;
4589      - add MATRIX_OPTIONS.h
4590    o verification/matrix_example:
4591       To allow to split the domain in several tiles, change the domain size
4592        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
4593        Western side) of land points.
4594    o (*_)write_pickup:
4595      - fix few bugs in mypackage_read/write_pickup.F
4596      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
4597        array of length 1 (was caught by compiler syntax-check).
4598    o pkg/diagnostics (velocity potential solver):
4599      - fix initialisation of main diagonal matrix (for overlap values)
4600    o tools/build_options:
4601      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
4602        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
4603      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
4604        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
4605        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
4606        and use "-devel" testreport option for standard testing on baudelaire.
4607    o pkg/grdchk:
4608      - Assume that all gradient-check position are within the same tile
4609        corresponding to global indices (iGloTile,jGloTile) and that
4610        positions (i,j indices or nbeg) are local to this tile;
4611      - set tile local-indices and proc. number according to tile global-indices;
4612      - remove grdchkwhichproc from namelist (retired param);
4613      - send adjoint gradient to all procs so that all procs print it to STDOUT;
4614      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
4615    o adding package bbl (Bottom Boundary Layer)
4616      description in MITgcm/pkg/bbl/bbl_description.tex
4617      example/test experiment in MITgcm_contrib/bbl
4618    o adjoint verifications
4619      - changed 5 experiments to multi-tiles
4620        * global_ocean.90x40x15
4621        * obcs_ctrl
4622        * offline_exf_seaice
4623        * tutorial_dic_adjoffline
4624        * tutorial_tracer_adjsens
4625        changed reference output for those that crossed tile boundaries
4626        (changed choices of gradient check positions)
4627      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
4628      - temporary bug fix in grdchk_loc.F for obcs
4629    o genmake2 & testreport
4630      - add target "obj" (just for OBJFILES files) to Makefile;
4631      - add option to specify FEXTRAFLAGS on command line.
4632    o pkg/mypackage:
4633      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
4634    
4635    checkpoint63a (2011/08/02)
4636    o pkg/diagnostics (velocity potential):
4637      - fix velocity-potential calculation when using OBCS: balance net inflow
4638        at each level (new S/R OBCS_DIAG_BALANCE).
4639      - fix some of the problems with OBCS in stream-function calculation.
4640    o pkg/exf/exf_readparms.F
4641      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
4642        EXF_NML_OBCS) more consistent, so that you need not have these lists
4643        in data.exf when they are not used.
4644    o optim/optim_readdata.F:
4645      - add some output about obcs variables that might help debugging
4646      - add a check about nvarlength
4647    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
4648    o pkg/diagnostics (velocity potential):
4649      - fix mask for OBCS (still problems in stream-function with OBCS);
4650      - add specific parameter (default = main code CG2D params) for solver;
4651      - in case of poor convergence, use solution corresponding to lowest residual.
4652    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
4653      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
4654      and should be avoided where possible.
4655    o model/src (rStar):
4656      - include r* effect on reference-state (PhiRef) in totPhiHyd
4657        (so that it's really the potential anomaly at the cell center);
4658        affect solution only if z* with full pressure in EOS.
4659      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
4660        update output (because of z* in totPhiHyd and viscA4 changes);
4661      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
4662        @ constant r) until interpolation at constant r is implemented.
4663    o pkg/diagnostics
4664      - fix RCENTER diagnostics in case cell center is not at interface middle
4665    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
4666      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
4667      that THETA and SALT are "conservative temperature" and "absolute
4668      salinity"
4669    o pkg/ctrl
4670      - fix computation of endrec in s/r ctrl_init_rec
4671      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
4672    o pkg/seaice/seaice_growth.F
4673      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
4674        remove then obsolete STORE directives
4675      - fix STORE directives for tice and tices, so that only the
4676        appropriate part of the fields are stored (and not the entire
4677        field); update global_ocean.cs32x15.seaice AD output.
4678      - cosmetic changes: adjust CPP flags and indentation for better
4679        legibilty
4680    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
4681      Chris Wilson)
4682    o pkg/gmredi:
4683       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
4684       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
4685    
4686    checkpoint63  (2011/07/11)
4687    o pkg/exch2:
4688     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
4689     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
4690       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
4691       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
4692    o pkg/diagnostics:
4693     - deal with pairs of post-processed diags which are computed together; in
4694       particular, re-order list of diags within 1 file to save 2nd computation.
4695     - add S/R to compute velocity stream-function (called after velocity-potential
4696       calculation) from divergence free transport -> new diagnostics "PsiVEL".
4697     - add parameter to select grid-point location where PsiVEL == 0.
4698    o eesupp/src:
4699       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
4700       (specific S/R needed with exch2 topology - for now, just print an error msg)
4701    o pkg/shelfice
4702     - Implement friction velocity-dependent transfer coefficients following
4703       Holland and Jenkins, JPO, 1999
4704       Original code by M. Losch with small modifs.
4705       Enable with CPP option SHI_ALLOW_GAMMAFRICT
4706       and runtime flag SHELFICEuseGammaFrict
4707    o verification lab_sea & global_ocean.cs32x15:
4708     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
4709       does not miss some dependencies (but is slower) and also works with many files
4710       (default makedepend limitation for AD built).
4711     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
4712    o pkg/diagnostics:
4713     - add run-time parameter "useMissingValue" (def=False) to fill land-point
4714        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
4715       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
4716     - Extend the use of "missing_value" setting from data.diagnostics for the case
4717       of counter-diagnostics (where fraction-weight is zero). This applies both to
4718       MNC and MDS output files.
4719    o pkg/seaice/seaice_growth.F:
4720      - add 'a priori' cap of latent heat flux based on actual mass considerations
4721        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
4722        non-legacy seaice_solve4temp.
4723      - add diagnostic of the residual sublimation freshwater flux (the freshwater
4724        flux taken from the ocean if the total actual latent heat fluxes exceed
4725        the maximum)
4726      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
4727       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
4728      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
4729       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
4730      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
4731      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
4732    o verification 1D_ocean_ice_column:
4733       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
4734       update results
4735    o pkg/diagnostics:
4736     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
4737       which are not filled-up but computed from other diags ; In this case, the mate
4738       diag points to the primary (filled-up) diag to used for post processing.
4739     - Update Velocity-potential computation using post-processed diag framework.
4740     ==> Change the ordering of fields and time-periods in MDS output file
4741       when using periodic averaging: now writes one time record with the full set
4742       of fields for this time period, then the next time reccord (it used to be
4743       one field with the full set of time records then the next field).
4744         Note: this is now similar to NetCDF (MNC) output file. <==
4745    
4746    checkpoint62z (2011/06/21)
4747    o adjoint monitor:
4748     - Add adjoint monitor output for packages exf, seaice
4749       and update relevant testreport output
4750    o pkg/seaice:
4751     - re-order diags inits so that they appear in order in available_diagnostics.log
4752     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
4753       area/heff/hsnow preceeding thermodynamic growth/melt.
4754     - modified diag: SIdA; output actual effect, as the description states.
4755     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
4756     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
4757       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
4758        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
4759     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
4760     - added diagnostics for seaice generic tracers (SItr*).
4761     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
4762     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
4763     I. Fenty: 18-Jun-2011:
4764     Minor changes to seaice package:
4765     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
4766        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
4767       - Differentiated "regularization variables" from "floor variables"
4768        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
4769        * hiceMin became SEAICE_hice_reg (old hiceMin)
4770          (with _reg meaning regularization variable)
4771       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
4772        so as to ensure energy conservation when going between phases
4773      - A22 was not used anywhere
4774     2) Changed regularization procedure for heffActual and hsnowActual to ensure
4775        well-boundedness and smooth adjoint in seaice_growth.F
4776     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
4777        because the old regularization always set heffActual >= 0.05 cm
4778     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
4779        on AREA when HEFF > 0.
4780      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
4781        requiring that DISABLE_AREA_FLOOR *not* be defined
4782     Affected verifications:
4783      - 1D_ocean_ice_column (output.txt output_adm.txt)
4784      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
4785    o pkg/diagnostics:
4786      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
4787      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
4788        (was _RL, now integer) with option = 0 to retrieve all levels.
4789      - add pieces of code to compute velocity potential at each level (new diagnostics
4790        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
4791        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
4792      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
4793        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
4794        and in diagnostics_fract_fill.F (do not need a valid pointer for the
4795        diagnostics counter-mate); check that definition of counter-diagnostic
4796        includes a valid counter-mate (in diagnostics_set_levels.F).
4797    o model/src (rStar):
4798      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
4799        affect solution only if z* with full pressure in EOS;
4800        update output of test-exp global_ocean.90x40x15.
4801    o pkg/seaice:
4802      - introduce siEps=1e-5 parameter
4803      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
4804      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
4805      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
4806        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
4807        as well as ice cover age and ridging index (attached to AREA).
4808        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
4809        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
4810        Up to SItrMaxNum=3 tracers can be used simultaneously.
4811    o pkg/salt_plume:
4812      -introduce SPsalFRAC run time parameter that sets the fraction of the
4813       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
4814       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
4815    o model debug options:
4816      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
4817        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
4818      - Refine debug-msg printing selection (3 new levels):
4819        debugMode  : controls printing of debug messages (sequence of S/R calls).
4820        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
4821         debLevZero =  0 ; /* level of disabled aux. msg printing */
4822         debLevA =  1 ; /* level of minimum  aux. msg printing */
4823         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
4824         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
4825         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
4826         debLevE =  5 ; /* level of extensive debug printing */
4827        New debugLevel default: with default debugMode value (=F),
4828          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
4829          and if debugMode=T, default debugLevel = 4 (debLevD).
4830        Relation with previous settings:
4831         debLevB (=2) corresponds to former debLevA (=1)
4832         debLevD (=4) corresponds to former debLevB (=2)
4833        Note:
4834         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
4835         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
4836            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
4837      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
4838        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
4839    o pkg/obcs:
4840      - change OBCSfixTopo default from True to False (should not change the results);
4841        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
4842    o pkg/thsice:
4843      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
4844        2nd layer seaice sublimation (unlikely to happen)
4845      - use Interior mask for OBCS in thsice_advection.F (similar to what is
4846        done in gad_advection & seaice_advection).
4847    o adjoint:
4848      bug fix spotted by Gael Forget:
4849      seaice_advection and thsice_advection still had
4850      legacy CPP options to avoid CS corner updates for adjoint
4851    o pkg/seaice:
4852      => Change some of the defaults (2011/05/29):
4853         - change SEAICEuseFluxForm default (from False to True)
4854         - change DIFF1 default (from 0.004 m/s to 0. m/s)
4855         And print warnings if DIFF1 is not set in data.seaice and centered
4856          avection scheme is used without any diffusion.
4857      also:
4858      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
4859      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
4860      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
4861        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
4862        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
4863      update results of test exp.:
4864         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
4865             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
4866             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
4867         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
4868         seaice_obcs: output (SEAICEuseFluxForm=T)
4869      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
4870          for standard fwd & AD lab_sea tests (to keep the same output).
4871    o pkg/seaice/seaice_growth.F:
4872      - use Ian Fenty's capping formulas for actual ice
4873      thickness thoughout EVOLUTION branch.
4874      - put treatment pathological case #2) in CPP brackets
4875      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
4876      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
4877    o pkg/seaice:
4878      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
4879      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
4880      also pass fac as a param, which can be 1. (to update the tendency
4881      field) or the time step (to update the field itself).
4882      - seaice_advdiff.F: for multidim, call seaice_diffusion with
4883      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
4884      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
4885      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
4886      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
4887    o pkg/seaice:
4888      diffusion with centered advection scheme (diffus.F & advect.F):
4889      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
4890        to just compute the laplacian of input-field.
4891      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
4892      - fix flux-form version in diffus.F to conserve tracer.
4893      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
4894       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
4895    
4896    checkpoint62y (2011/05/26)
4897    o pkg/seaice:
4898     - seaice_growth.F : in EVOLUTION branch, always include
4899       a_QSWbyATM_cover in qnet (as it should be).
4900     - verification/global_ocean.cs32x15 : update results accordingly
4901       (output.seaice.txt output_adm.seaice.txt).
4902    o pkg/seaice + obcs:
4903     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
4904       equivalent of assuming no tracer gradient outside the OB region.
4905       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
4906     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
4907       after changes above);
4908     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
4909       only at OB location (instead of over a band of OLx width).
4910    o pkg/seaice:
4911     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
4912       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
4913    o pkg/obcs:
4914      - split header file "OBCS.h" into 4 separated files:
4915        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
4916       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
4917         (contain no conditional statement which depends on OBCS options).
4918      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
4919        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
4920    o ctrl, cost, grdchk & autodiff pkgs:
4921      - make options file more standard (like other {PKG}_OPTIONS.h file but
4922        with AD_CONFIG.h); clean-up some of the included header files.
4923    o pkg/obcs:
4924      - do not mask tracer when applying OB (tracer == 0 could generate problems)
4925      - apply tracer OB values to tracer field only at OB location (instead of
4926        over a band of OLx width)
4927      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
4928      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
4929        obcs_apply_tloc.F & obcs_apply_sloc.F
4930    o obcs in model/src:
4931      - call OBCS_APPLY_W only if NonHydrostatic.
4932      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
4933      - reset dEtaHdt and wVel to zero outside OB interior region ;
4934      - leave tracer unchanged outside OB interior region: This has no effect
4935        on the solution but just to prevent unrealistic tracer value outside OB.
4936      - zero out velocity outside OB interior region: This has no effect on
4937        the solution but just to prevent unrealistic velocity outside OB.
4938    o obcs and non-lin free-surf:
4939       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
4940       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
4941       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
4942       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
4943       update results of test-exp. exp4(nlfs).
4944    o exp4 (nlfs) test-exp:
4945       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
4946       with NonLin-FreeSurf); update output.nlfs.txt
4947    o obcs and 2d/3d solver norm:
4948       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
4949       and outside OB interior region (will allow to place OB further inside the
4950       domain). Depending on the domain, can affects cg2d-Norm (previous
4951       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
4952       and cg3d-Norm (previous Norm was computed before canceling OB terms),
4953       e.g. in tutorial_plume_on_slope.
4954      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
4955    o pkg rbcs:
4956      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
4957      - add capability to apply relaxation to horizontal velocity uVel & vVel.
4958    o pkg/grdchk: add gradient check for control variable xx_shifwflx
4959    o pkg/shelfice/shelfice_init_fixed.F
4960      fix CPP-flag combinations
4961    o pkg/seaice: Merge iceage code of Pierre Rampal
4962      * update/change/correct ice age calculations
4963      * add age updates for pathological cases
4964      Probably needs more testing...
4965    
4966    checkpoint62x (2011/05/13)
4967    o pkg/mom_vecinv:
4968       high-order vorticity scheme: use interior masks (maskInW & S)
4969       to zero-out (outside OB) gradient of vorticity.
4970    o verification exp.:
4971       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
4972       hs94.128x64x5 and seaice_obcs ; update results.
4973    o pkg/obcs:
4974      fix bug in OBeta for YZ sections in obcs_exf_load.F
4975    o pkg/ctrl, pkg/shelfice, and optim:
4976      - add new control variable xx_shifwflx (fresh water flux underneath ice
4977        shelves). This is almost as tedious as obcs-ctrl, because the
4978        variables needs its own mask.
4979      - add a cost function term that penalizes the deviation of xx_shifwflx
4980        from the first guess (zero) in analogy to other control variables
4981    o pkg/shelfice:
4982      - start basic adjoint
4983    o pkg/ctrl:
4984      - remove extra 2D field "for good measure" when initializing in
4985        ctrl_set_globfld_[xy/xz/yz].F
4986      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
4987      - improve error messages in ctrl_set_unpack_*
4988    o OBC implementation in momentum:
4989       use interior masks (maskInC,W & S) in momentum S/R:
4990       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
4991       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
4992       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
4993       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
4994       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
4995        (and also with Leith/Smagorinsky harmonic-viscosity).
4996       Update output of experiment dome and exp4 (+nlfs).
4997    o exp4 test-exp:
4998      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
4999        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
5000        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
5001        time-varying OB at Western-side for wVel (NonHyd); update output.
5002      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
5003        and biharmonic-viscosity ; also use prescribed time varying OB.
5004    o pkg/obcs:
5005      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
5006    o model/src:
5007      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
5008      - initialise startTime & nIter0 with unlikely values: allows to set one
5009        from the other without ambiguity.
5010    o seaice_obcs test-exp.:
5011      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
5012    o pkg/obcs:
5013      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
5014        no longer needed with maskInC,W,S in pkg/generic_advdiff.
5015    o pkg/seaice:
5016      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
5017        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
5018      - fixed bug in the initialization of sea ice salinity variable HSALT
5019        in seaice_init_varia.F  (removed dependence on ICE2WATR)
5020    o fizhi-cs test exp.:
5021       switch reference output convention for these 2 non-standard test-exp,
5022        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
5023          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
5024       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
5025    o model/inc:
5026      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
5027        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
5028    o pkg/seaice:
5029      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
5030    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
5031      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
5032        and initial HSALT
5033    
5034    checkpoint62w (2011/04/26)
5035    o pkg/mom_fluxform:
5036      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
5037      - use parameter "sideDragFactor" in no-slip BC side-drag part.
5038      - update output of exp. global_ocean.90x40x15
5039    o pkg/mom_vecinv:
5040      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
5041    o update seaice exp.:
5042      use more consistent parameter values (remove "backward compatability only":
5043       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
5044      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
5045       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
5046    o update test-exp global_ocean.90x40x15:
5047      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
5048      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
5049      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
5050      o turn on zStar & viscA4 in standard set-up (dir input/)
5051        and update output files: output.txt & output.dwnslp.txt
5052    o new AD-test experiment: obcs_ctrl
5053      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
5054    o pkg/dic:
5055      fix two bugs in handling water vapour pressure in carbonate chemistry
5056      and air-sea fluxes. Found by Val Bennington and Galen McKinley
5057      (add DIC Option = WATERVAP_BUG to recover old results)
5058      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
5059    o adding allowInteriorFreezing option to check for water below freezing point
5060      at depth and bring the negative heat anomaly to the surface level
5061    o pkgs _fields_load:
5062      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
5063      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
5064        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
5065        rbcs to get interpolation weights and time reccord number.
5066      - fix multi-threading in aim_fields_load.F
5067      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
5068    o external_fields_load:
5069      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
5070       interpolation weights) to use in a periodic time-series ; do not divide by
5071       time-step to convert to integer:
5072       - this fixes case where externForcingPeriod is not multiple of time-step
5073          (Thanks to Christopher L. Wolfe)
5074       - this fixes case where externForcingPeriod is an odd multiple of time-step
5075         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
5076      store index of time-record which is currently loaded:
5077       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
5078       - needed for the adjoint but not yet used because of extensive recomputations;
5079         (to be fixed soon)
5080    
5081    checkpoint62v (2011/04/02)
5082    o verification/1D_ocean_ice_column added to test Ian Fenty's
5083      pkg/seaice_growth.F modifications for improving sea ice code differentiability
5084    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
5085      (new velocity statistics after changing maskInW & maskInS definition)
5086    o pkg/generic_advdiff with OBCS:
5087      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
5088      equivalent to assumption of no tracer gradient outside the OB region.
5089      This will affect the results if using obcs+biharmonic diffusion.
5090      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
5091    o pkg/obcs:
5092      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
5093      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
5094      in Interior region. No impact on solution but affects Velocity monitor stats.
5095    o pkg/ptracers (adjoint)
5096      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
5097      tape file for each tracer
5098    o model/inc/src and pkg/autodiff: add parameters that allow to turn
5099      of parts of the adjoint code at run time. For now, there are only
5100      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
5101      parameters are set in data.pkg.
5102      This is the lazy coward's version of doing this, but still useful for
5103      debugging. In order to do it right, everything needs to be moved to
5104      pkg/autodiff.
5105    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
5106      the end; this fixes the adjoint balancing code for open boundaries.
5107    o pkg/ctrl:
5108      - change behavior of xx_${varname}period to be analogous to exf-conventions:
5109        xx_${varname}period =   0.,  means time-independent control part
5110        xx_${varname}period = -12., means one-year-periodic monthly control part
5111      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
5112        clean up ctrl_init a little, remove unused variables
5113      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
5114      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
5115    
5116    checkpoint62u (2011/03/15)
5117    o model/src:
5118      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
5119        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
5120      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
5121        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
5122    o pkg/ctrl/obcs/ecco:
5123      - remove obsolete, unused, and partially broken code:
5124        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
5125        ALLOW_CTRL_OBCS_BALANCE
5126      - put a stop statement into ecco/cost_obcsvol.F, but also add
5127        cost_obcsvol to ecco_ad_diff.list
5128    o pkg/ecco: fix counting cost function contributions for obcs (code
5129      by Matt M.) and diffkr for diagnostics
5130    o pkg/ecco, pkg/ctrl, pkg/grdchk:
5131      add cost penalty terms for initial uvel, vvel, eta controls
5132      and I/O for prior error files
5133    o pkg/mdsio:
5134       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
5135       (new argument) to check for tiled file in mdsioLocalDir : this fix the
5136       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
5137    o pkg/ctrl:
5138     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
5139       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
5140       unused and superfluous variables
5141     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
5142    o pkg/ecco
5143     - enable adjoint of Stevens OB
5144    o pkg/ctrl/ecco/grdchk:
5145      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
5146        Fortunately, we do not have any tests for the numerous cpp-flagged
5147        option of "obcs as control parameters" so we will never know
5148        if this is an improvement (but at least now things compile).
5149      - remove an obsolete initialization from ecco_cost_init_barfiles.F
5150      - fix some problems within never used ifdefs to make the code compile
5151    o pkg/obcs:
5152     - Refine Interior mask definition to work with more complex OB (e.g.
5153       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
5154       read in Interior mask from file. Check if Interior mask is consistent
5155       with OB list of indices.
5156    o pkg/seaice
5157     - beginning code for a seaice tracer package,
5158       but currently only used for seaice age: SEAICE_AGE
5159       SEAICE_num = 4
5160       iTracer = 1: area-weighted ice age
5161               = 2: volume-weighted ice age
5162               = 3, 4: template for one-year vs. multi-year ice
5163       data.seaice has new namelist SEAICE_PARM03 for arrays related to
5164       SEAICE_num
5165    
5166    checkpoint62t (2011/03/05)
5167    o pkg/obcs:
5168     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
5169       then normal component. This ensures that the normal component is set
5170       correctly even when it conficts with tangential setting from an other OB.
5171       Affects results of test-experiment seaice_obcs: update the output.txt
5172    o pkg/obcs:
5173     - add code to monitor statistics of dynamical fields at OB.
5174     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
5175       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
5176       - change default: balance the Net inflow through all OB (instead of balancing
5177         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
5178     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
5179       to match Nortern OB inflow (OBCS_balanceFacN=0).
5180    o pkg/seaice:
5181     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
5182    o pkg/seaice (seaice_growth v 1.113):
5183     - reverting seaice_growth to v 1.111 in order to have code with exact bit
5184       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
5185       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
5186       runtime flag SEAICEareaFormula is kept but is inactive
5187    o model/src:
5188     - add new param to scale curvilinear grid distance and area when using
5189       a different sphere radius from the grid-files.
5190     - test/check multi-threads EXCH applied to local variable (cg2d_x)
5191    o adjoint:
5192     - enable adjoint of Stevens OB
5193     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
5194       (a bit delicate because of potentially modified adj. common block structure;
5195       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
5196    
5197    checkpoint62s (2011/02/15)
5198    o pkg/seaice (seaice_growth v 1.112):
5199     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
5200       computing the ice cover tendency from effective thickness tendencies. Include
5201       Ian Fenty's formula.
5202     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
5203       SEAICEareaFormula.
5204     - simplify notations for the various d_HEFF/d_AREA terms.
5205    o pkg/gmredi:
5206     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
5207       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
5208       add a verification test-run (front_relax.bvp) to test GM_useBVP.
5209    o pkg/seaice (seaice_growth v 1.111):
5210     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
5211     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
5212       also melt ice.
5213    o pkg/seaice:
5214     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
5215     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
5216    o pkg/cheapaml:
5217     - from Nico Wienders: New version of this package.
5218    o pkg/flt:
5219     - add CPP options to prevent floats to re-enter the opposite side of
5220       a periodic domain (default: keep periodicity)
5221    o pkg/gmredi:
5222     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
5223       (needed for multi-dim advection).
5224     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
5225    o model/src:
5226     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
5227    o tutorial_tracer_adjsens
5228     - extend to NLFS and replace maskC by hFacC
5229       (change reference output accordingly)
5230    
5231    checkpoint62r (2011/01/24)
5232    o testreport:
5233     - add option -deloutp (-do) to remove output file after successful run
5234     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
5235       extract exact list of procs from this file ; adjust COMMAND by
5236       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
5237    o pkg/ecco: replace old ineffective way of penalizing deviations from
5238      first guess (of obcs) with code by Matt Mazloff
5239    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
5240      exf/cal
5241      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
5242        and handle case of obcs?period == 0
5243        Not affected by these changes: There is still an inconsistency in
5244        the computation of start/endrec for the obcs variables for ALLOW_CAL
5245        defined (see comment by Menemenlis, 7-Mar-2003)
5246      - make S/R ctrl_get_gen_rec return something meaningful even if
5247        ALLOW_CAL is not defined
5248      - ctrl_getobcs?: simplify code so that it does not need to use
5249                       S/R exf_swapfields
5250    o testreport:
5251       allow to test MPI with different number of processors for each experiment:
5252       create file "SIZE.h.mpi" in each build dir.
5253       Note: update of "-command" argument not yet implemented.
5254    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
5255      alleviate the need for additional 3D tapes when using
5256      the non-inear free surface in the adjoint. This is done
5257      by adding an 'update' of hfacc etc. to their current
5258      value at the beginning of forward_step.F.
5259    o pkg/seaice
5260      seaice_lsr: move stress-divergence computations out of outer pseudo-
5261      timestepping loop
5262    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
5263      up, so that the calls of the ctrl_* subroutines are really at the end
5264      of the routine.
5265    o pkg/gmredi:
5266      allow to specify a 2-D horizontal map and a 1-D vertical profil
5267      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
5268    o pkg/seaice:
5269      move lsr iterations from seaice_dynsolver to seaice_lsr.
5270    o pkg/seaice:
5271      reduce memory footprint of seaice mutldim advection tapes,
5272      by using a 2D tape independent of the generic_advdiff ones,
5273      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
5274    
5275    checkpoint62q (2010/12/29)
5276    o model/src:
5277      - check horizontal grid-spacing for unset or zero/negative values.
5278      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
5279    o pkg/flt:
5280      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
5281      - precision of input and output files set according to readBinaryPrec
5282        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
5283      - initial float position from tiled file was not converted to index space
5284        (looks like a bug): fixed to make it similar to initial pos. global file.
5285    o global_ocean.cs32x15:
5286       change SIZE.h of AD set-up to get same tiling as with MPI.
5287       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
5288    o model/src:
5289       add flag to control printing of domain fields (bathymetry, hFac ...) in
5290       ini_mask_etc (call to plot_fieds_xy*).
5291    o pkg/thsice:
5292       if useEXF, some forcing fields are not valid in overlap: fixed by computing
5293       over the interior only + apply EXCH at the end (like with SEAICE advection).
5294    o pkg/mdsio:
5295      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
5296        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
5297      - change barrier call for safe multi-threads access to 3-D shared buffer.
5298      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
5299      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
5300        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
5301    o pkg/flt:
5302      - add fourth-order Runge-Kutta integration
5303      - add basic exch2 support (only 1 facet supported so far!)
5304    o pkg/mdsio+rw:
5305      new S/R to read local (or tile independent) vector (read counterpart of
5306       mds_writevec_loc, and front-end write_glvec_rl/rs).
5307    o global_ocean.cs32x15: additional input_ad.seaice experiment
5308        that uses pkg/seaice rather than pkg/thsice.
5309        (using multidim advection for seaice)
5310    o towards more F95 syntax for array specification in namelist:
5311      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
5312        of all verification experiments.
5313           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
5314          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
5315      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
5316    o global_ocean.cs32x15: additional input.seaice experiment
5317        that uses pkg/seaice rather than pkg/thsice.
5318    
5319    checkpoint62p (2010/12/17)
5320    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
5321        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
5322    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
5323        allow for use of multim. advection in seaice adjoint.
5324    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
5325      - first attempt to close budgets by taking into account the freshwater
5326        flux implied by the sublimation of snow and ice. So far only the
5327        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
5328        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
5329    o eesupp/src:
5330      new S/R with new option (NML_EXTENDED_F77) to change array specification
5331      from F95 standard to commonly accepted extended F77 form.
5332      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
5333      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
5334      for less tolerant f77 compiler (e.g., pgf77, g77).
5335    o globalFiles:
5336      commented out in parameter file "data" since it's not safe with MPI
5337      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
5338      in this case); no longer commented out in restart test (tst_2+2).
5339    o add adTapeDir to specify a special directory where adjoint tapes are
5340      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
5341      and cannot be used together with mdsioLocalDir.
5342    o nesting pkgs:
5343      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
5344      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
5345      - add parameter files + utils dir + output from short run on beagle.
5346    o pkg/seaice:
5347        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
5348    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
5349      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
5350    
5351    checkpoint62o (2010/11/25)
5352    o pkg/exf:
5353      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
5354    o pkg/seaice:
5355      - seaice_ocean_stress: split a loop for better vectorization of the
5356        adjoint code
5357      - seaice_growth.F: fix bug in conservation of freshwater connected to
5358        capping of heff, put contribution into d_HEFFbyNEG
5359      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
5360        by something more sensible (parameters that are what their name implies)
5361      - change some defaults, so that by default exf-parameters are used for
5362        things like rhoAir, cpAir,latent/sensible heat parameters, in order
5363        to reproduce the old results, many data.seaice now contain funny values
5364        for cpAir and latent heat of sublimation
5365    o packages_readparms.F: move exf_readparms up in line so that
5366        exf-parameters are visible for other packages (e.g. seaice)
5367    o debugMode & debugLevel=2:
5368      - differentiate between debugMode & debugLevel=2:
5369        debugMode: controls printing of debug messages (sequence of S/R calls).
5370        debugLevel: controls printing of algorithm intermediate results and stats.
5371      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
5372        => allows to print debug-stats without all sequence of call messages.
5373      - switch control of debug print from debugLevel to debugMode in many S/R.
5374    o pkg/obcs (obcs-sponge):
5375        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
5376        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
5377    o pkg/generic_advdiff:
5378      - record overlap minimum size for each advection scheme;
5379      - refine criteria on overlap minimum size;
5380      - check and stop (in gad_check) if overlap size is too small.
5381    o pkg/obcs:
5382      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
5383        once, in ptracers_implicit.F)
5384      - with seaice: remove test on empty file name in obcs_apply_seaice (always
5385        apply OB values when tile has OB)
5386    o model/src, coriolis setting:
5387      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
5388        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
5389        files (selectCoriMap=3) with any grid.
5390      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
5391    o pkg/seaice/seaice_growth.F:
5392        a few cosmetic changes that reduce the number of lines of code
5393    o pkg/obcs: add boundary conditions following Stevens (1990)
5394      - the code follows old MOM/NAOSIM code
5395      - so far it is only implemented for the eastern and western boundaries
5396        and NOT for pTracers
5397    o pkg/rbcs:
5398      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
5399        beginning of the first rbcs forcing period.
5400      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
5401        offline package, i.e., one file per time, labeled by iteration number;
5402        deltaTrbcs sets the timestep with which the data was generated;
5403        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
5404      - rbcsForcingCycle=0 makes forcing non-cyclic.
5405      - make arithmetic safe for negative times and odd forcing periods.
5406    
5407    checkpoint62n (2010/11/09)
5408    o pkg/seaice:
5409        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
5410    o pkg/obcs:
5411       New S/R to copy tracer value from the OB location to narrow band region
5412        (width = same as overlap) beyond the OB: preserve OB value (needed for
5413        high-order scheme) which were overwritten by EXCH call if in overlap
5414        region. Applied to theta, salt, ptracer and advected seaice variables.
5415       With seaice: use maskInC in similar way as in gad_advection.F,
5416        in seaice_advection.F and advect.F.
5417       Update output of experiment seaice_obcs and change exp4 to test OBCS with
5418        4th order Adv.Scheme. for pasive salt and ptracer.
5419    o tools/genmake2:
5420      - when looking for an optfile (not specified), only search for Fortran compiler
5421        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
5422      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
5423        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
5424      - set default for CPP to "cpp -traditional -P" (was the case without specifying
5425        an optfile, but otherwise default was just "cpp".
5426      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
5427      - when "CC" is not set in the optfile, look for possible C compiler
5428        (instead of just setting CC=cc)
5429      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
5430        => add a ".F" to ".o" rule for source files with no "#include" (such as
5431           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
5432      - move gfortran before g77 in list of possible Fortran compiler (consistent
5433        with reference compiler switch from g77 to gfortran)
5434    o pkg/seaice:
5435      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
5436        seaice_check that stops the model, when the CPP flag is used.
5437      o seaice_growth.F: make capping of ice volume conserving by returning the
5438        capped ice as freshwater to EmPmR. This does not change the verification
5439        experiments but will change runs where the capping is acutally active
5440    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
5441      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
5442         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
5443         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
5444    o tools/genmake2:
5445      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
5446      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
5447      - clean previous genmake log files before anything else.
5448      - change Makefile to remove testreport log files (*.tr_log) and genmake log
5449        files only with "CLEAN" target (instead of "Clean");
5450    o pkg/generic_advdiff:
5451      Change OBCS in multiDim advection (gad_advection.F):
5452       Use maskInC to prevent intermediate update of tracer-field in OB regions,
5453       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
5454       which were applying future time-step OB values.
5455      This way, all explicit calculations use current-time-step OB values
5456       (simpler and more consistent).
5457      Affects results when set-up uses time-varying OBC and multi-dim advection;
5458       update output of experiment seaice_obcs.
5459    o pkg/seaice:
5460      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
5461       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
5462         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
5463      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
5464       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
5465       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
5466    o pkg aim (2010/10/26):
5467      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
5468        formulation with obliquity, eccentricity, ... as run-time parameters,
5469      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
5470        upward shortwave radition at the surface (all-sky and clear-sky).
5471    o pkg/obcs:
5472      - writing sections with globalFiles=T does not work: switch to tiled-files
5473        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
5474      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
5475      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
5476    
5477    checkpoint62m (2010/10/21)
5478    o pkg/seaice: vectorize seaice_solve4temp.F
5479      - move iterations loops outside of i/j-loops
5480      - requires 2D arrays for TB and effConduct
5481      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
5482        modified in this routine
5483      - a little bit of clean up, adjusting indentation, etc.
5484      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
5485        performance and '**TWO' by '**2' (because TWO is a float),
5486        replaced ONE, ZERO
5487    o eesupp/src:
5488       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
5489    o pkg/seaice/seaice_growth.F
5490      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
5491      merging process. The merged routine has two branches, and one activates the 'evolution'
5492      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
5493      In summary, here is what the '10/10 revision' did consist of
5494        part 1: seaice_growth.F revisions 1.71 to 1.75
5495          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
5496            The emphasis here was on improving readability (e.g. by trying to use meaningful
5497            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
5498        part 1.5:
5499          - revising the lab_sea experiment to make it a more useful (i.e. stable
5500            and representative of an actual model run). This was done by generating a
5501            (winter) pickup to start from, switching back the main experiment dynamic
5502            solver from evp to lsr, having one of the experiments use the free drift solution.
5503        part 2: seaice_growth.F revisions 1.76 to 1.85
5504          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
5505          - Sorting out the various fields units and sign (set early on and reset at the end)
5506            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
5507            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
5508          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
5509            and simplifying logical expressions to further improve readibility.
5510        part 3: seaice_growth.F revisions 1.86 to 1.89
5511          - Re-organize the blocks of code more logically.
5512          - Merging the '_if.F' pieces that add something new.
5513    o pkg/thsice:
5514      - vectorize thsice_solve4temp and thsice_get_exf.
5515        Problem: thsice_solve4temp has an unvectorizable statement that
5516        might also be problematic for TAF
5517      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
5518        does not change the verifcation experiment, but will change all
5519        experiments that have this flag undefined (not tested in verification);
5520        a little reorganization to save a few 2D fields and recomputations
5521      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
5522      - 2nd step:  fix some store dirs
5523        o seems to work somewhat, i.e. using ifort but not g77
5524        o likely cause are incomplete init. or recomputation
5525        o start verification/global_ocean.cs32x15/input_ad.thsice
5526    o pkg/obcs: add support for exch2
5527      - the position of the boundary and prescribed values are specified using
5528        a global domain with exch2 facets stacked
5529        - in x for N,S boundaries (like W2_mapIO=-1)
5530        - in y for E,W boundaries (so E,W boundaries do not overlap)
5531    o pkg/mdsio: add support for writing global sections with exch2
5532        file layout is as for obcs described above:
5533        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
5534        - for y-z sections, facets are stacked in y
5535    o pkg/thsice:
5536       - change a few routines for better vectorization: thsice_albedo.F,
5537         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
5538         not affected, but in particular the latter routine has changed
5539         dramatically (not necessarily easier to read now).
5540       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
5541       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
5542    o verification/lab_sea:
5543      - overhaul of the forward model experiments. The main motivation
5544        for this revision is that lab_sea has proven quite fragile (when
5545        changing the sea-ice code, and switching platforms) to a point
5546        when failures were very hard to attribute to specific code problems.
5547      - the suspected reason for this fragility is noise amplification by evp so,
5548        to start with, we decided to replace evp with lsr in the main experiment.
5549      - the input.lsr experiment thus became obsolete and was removed.
5550      - it was replaced with the input.fd experiment that uses an
5551        analytical "free drift" solution as the ice velocity field.
5552      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
5553        will hopefully allow us to discriminate problems due to dynamic solvers
5554        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
5555        us to test additional options, along with the salt plume package.
5556      - Finally a pickup was generated (at the end of a one year run) to
5557        make the tests more representative of an actual model run. Previously
5558        the tests starting point was a 1m thickness of ice everywhere.
5559    o pkg/seaice:
5560      - introducing S\R seaice_freedrift.F that compute the
5561        analytical solution to an approximate ice momentum
5562        equation (i.e. the simple stress/coriolis balance).
5563      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
5564        of the free drift velocity field, and enable its use.
5565        To actually use the free drift solution as the model ice
5566        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
5567    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
5568    
5569    checkpoint62l (2010/10/04)
5570    o pkg/seaice:
5571      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
5572      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
5573       version (with USE_ORIGINAL_SBI undef);
5574    o add hooks for new packages OASIS, the package will follow
5575      (hooks exclude the seaice pkg for now)
5576    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
5577      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
5578      rather than mdsio_readvector.F/mdsio_writevector.F, within
5579      adread_adwrite.F to read/write adjoint-related tapes to disk.
5580    o eesupp and pkg/mdsio: ALLOW_WHIO
5581      Option to write/read 2D fields to files including tiles halos.
5582      The main purpose is for adjoint related "tape I/O".
5583      The secondary purpose is for debugging phases.
5584      A word on those rather specifically intended purposes.
5585      The code was meant to be stripped down to the bare minimum.
5586      Typically, there is a unique and basic mapping to the global
5587      buffer (tile by tile, then proc by proc, then level by level), and
5588      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
5589      meant to generate user friendly outputs of various shapes and forms.
5590      Rather it is intended, for the knowledgeabale developers,
5591      to be largely independent of the many mdsio options, to allow
5592      outputs of tiles+halos in debugging phases and in adjoint runs,
5593      and to allow some flexibility in tuning (adoint) I/O depending on each
5594      file system behavior. With regard to tuning, most of the potential knobs
5595      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
5596      to specify directories, to specify the typical size of I/O calls, etc.)
5597      are not yet included, and will be added if they prove useful.
5598    o pkg/seaice:
5599       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
5600    o pkg/seaice:
5601       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
5602       code (seaice_budget_ice_if.F) which enable to recover old standard
5603       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
5604       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
5605    o model/src (rStar):
5606       use simple average (not area weighted) of rStarFac at U,V point when using
5607       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
5608       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
5609    
5610    checkpoint62k (2010/09/17)
5611    o adjoint
5612       * changed verification/global_ocean.cs32x15 ; adjoint now tests
5613         Adams-Bashforth 3 + NLFS + RSTAR
5614       * some more modifs required for ECCO-GODAE v4
5615    o pkg/seaice
5616       add SEAICE_AGE_VOL option to use volume instead of area for
5617       integrating SEAICE_AGE
5618    o model/src:
5619       first check-in of sigma & hybrid-sigma coordinate code ; also includes
5620       non-linear free-surface parts ; but pressure-gradient not yet coded.
5621    o pkg/ptracers:
5622       option for ptracer to convert Salt Relax into additional EmP.
5623        tested in exp. global_ocean.90x40x15.dwnslp (update output)
5624    
5625    checkpoint62j (2010/08/25)
5626    o pkg/ggl90:
5627       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
5628    o pkg/dic: car_flux.F, phos_flux.F
5629      - reduce number of exp-calls in order to improve performance
5630      - clean up a little (replace fields by their macros, etc., fix
5631        typo in CPP-flag)
5632    o pkg/ggl90: minor changes
5633      - GGL90diffKrS was removed --> always use GGL90diffKr
5634      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
5635      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
5636        (commented out for now)
5637      - change in max/min operations to ensure that smoothing is ok
5638      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
5639      - always use diffKrNrT as background profile (i.e. never use diffKr field)
5640    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
5641    o pkg/dic:
5642      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
5643        vectorization
5644      - small bug fix in insol for the unlikely case of a cartesian grid
5645      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
5646        + now vectorize, which also removes adjoint recomputations;
5647        + replace integer maksp1 by _RL maskp1
5648        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
5649    
5650    checkpoint62i (2010/07/21)
5651    o pkg/flt:
5652      - with OBCS: stop floats which enter the OB region
5653    o model/src:
5654      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
5655        for implicit vertical advection.
5656    o pkg/seaice:
5657     - account for melting in seaice age evolution.
5658     - remove double counting of seaice ridging effect on seaice age.
5659    
5660    checkpoint62h (2010/06/18)
5661    o pkg/exch2:
5662     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
5663    o tools/genmake2
5664      - remove "-pdefault" option: redundant with the use of "packages.conf";
5665      - remove file pkg/pkg_default : set the default as a pkg group
5666        ("default_pkg_list") defined in pkg/pkg_groups;
5667      - fix for case pkg/pkg_depend is missing (was hanging before);
5668      - add option "-pgroups" to specify a different pkg_groups than the default.
5669    o verification/adjustment.cs-32x32x1:
5670       add a "minimal" set-up test (code_min & input_min) which only compiles
5671       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
5672    o tools/genmake2
5673      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
5674      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
5675    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
5676      files are nearly the same anyway.
5677      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
5678       - redefinition of tau(i,i) (by a factor of ustar)
5679       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
5680       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
5681       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
5682       - replace
5683         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
5684         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
5685         by
5686         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
5687         (changes results)
5688       -> exf_bulkformulae v1.22,
5689          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
5690          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
5691                    output.txt 1.63
5692           offline_exf_seaice: output.seaicetd.txt 1.7
5693           seaice_obcs: output.txt 1.10)
5694      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
5695       -> exf_bulkformulae v1.23,
5696          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
5697          and global_ocean.cs32x15.icedyn (only 11 matching digits)
5698      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
5699    o adjoint of exch-1:
5700     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
5701       (note: was already like this when using EXCH-2) and remove flow dir
5702       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
5703     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
5704     - update pkg/exch2 diff list.
5705    
5706    checkpoint62g (2010/05/19)
5707    o eesupp/src (exch-1):
5708     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
5709       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
5710       (renamed to exch1_*rx_cube.F).
5711     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
5712       to call new exch1 S/R ; update Makefile and .cvsignore.
5713     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
5714       exch2_xy_rx later)
5715      Note: after updating your code, need to run "make clean" in eesupp/src
5716    o test experiment bottom_ctrl_5x5:
5717       new output_adm.txt with fewer grdchk & less monitor output.
5718    o model/src:
5719      remove the call to ini_cori in initialise_varia.F (just keep the usual one
5720       in initialise_fixed.F). More consistent with coriolis & horizontal grid
5721       beeing treated in the same way (ini_grid is not called a 2nd time).
5722    o pkg/exf:
5723      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
5724      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
5725      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
5726      - cosmetic changes to exf_bulkformulae.F to make it look more like
5727        exf_bulk_largeyeager04.F
5728    o eesupp/src (exch-1):
5729      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
5730      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
5731        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
5732        (even without using MPI).
5733      - Message mode: move RecvAck setting (indicator of buffer being ready)
5734        from send_put to recv_get S/R (was useless before, but not sure if
5735        it's much more useful now);
5736      - Switch the order of sync: MPI-proc 1rst and then threads;
5737      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
5738      - fix AD code for communication mode ='get' (but not used).
5739    o model/src:
5740      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
5741      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
5742    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
5743    o pkg/ctrl: require a specific set of control variables and exf-flags for
5744      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
5745    o model/src:
5746     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
5747       1rst forward sweep, to avoid over-writing output files during recomputations
5748       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
5749     b) 2nd version:
5750      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
5751      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
5752         writePickupAtEnd) + seaice & ptracers output;
5753      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
5754    o model/src:
5755      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
5756    o pkg/exch2:
5757      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
5758      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
5759    o pkg/autodiff & exch2:
5760      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
5761      (for now, only if ALLOW_EXCH2 is defined).
5762    o pkg/autodiff:
5763      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
5764        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
5765       + clean-up comments (_RS is not always real*4)
5766      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
5767      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
5768        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
5769    o testreport (AD-tests):
5770      no longer link files from dir "../input" (1rst link files from
5771      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
5772    
5773    checkpoint62f (2010/04/29)
5774    o model/src/the_main_loop.F:
5775      adjust store directives for seaice evp and multicategory according to
5776      pkg/ecco/the_main_loop.F
5777    o adjoint:
5778      global_sum_ad was incomplete (noted many times by many people ;)
5779      nice description by Jean U. as follows:
5780      * allreduce(var) in global_sum.F can be interpreted as
5781        reduce(sum) followed by broadcast of sum.
5782      * The adjoint of that is
5783        sum(adjoint) followed by broadcast(summed adjoint value)
5784        or in other words, allreduce(sum, adjoint vars)
5785      We were missing the sum(adjoint)!
5786      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
5787      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
5788      The fix should produce 16-digit accuracy between
5789      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
5790      multi-CPU single-tile (e.g. nSx=1, nPx-2)
5791      We'll probably change this yet again shortly
5792    o eesupp/src:
5793      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
5794    o pkg/icefront
5795      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
5796        specification of addmass array based on a 2D field, which is added
5797        at bottommost wet level at each horizontal location.
5798    o model/src:
5799     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
5800     layout; (not always compatible with delX,delY setting; commented out for now).
5801    o pkg/exch2:
5802     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
5803     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
5804    
5805    checkpoint62e (2010/04/15)
5806    o pkg/obcs:
5807      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
5808    o pkg/dic:
5809      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
5810        (note: not presently tested in any forward verification exp.)
5811       update tutorial_global_oce_biogeo AD output file.
5812    o pkg/exf:
5813      - account for the variation of albedo as a function of zenith angle
5814        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
5815    o build_options:
5816     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
5817    o pkg/dic:
5818      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
5819      - use binary pickup file for restart;
5820      - initialise atmos-CO2 box from dic_pCO2 parameter;
5821      - fix multi-threaded.
5822    o pkg/rbcs:
5823     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
5824       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
5825     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
5826       and update output.txt
5827    o pkg/kpp:
5828     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
5829     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
5830       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
5831       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
5832     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
5833       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
5834    o pkg/offline:
5835      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
5836      (bug was added in version 1.10 on 2007-08-23).
5837    o pkg/offline:
5838      - no need to specify periodicExternalForcing, etc ... to use offline pack
5839      - offline input files no longer just single prec --> parameter offlineLoadPrec
5840    o verification/lab_sea:
5841      change AD test to multi-tile setup and update all 4 AD output.
5842      NOTE: while cost function values remain very similar,
5843      gradients are very different, although gradient checks are self-consistent
5844      Should try to get to the bottom of this (cost function summation order?)
5845    o pkg/dic:
5846      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
5847      a weakness of TAF that drops part of double precision in log10 derivative.
5848      <= changes removed since problem has been fixed in current TAF version 1.9.71
5849      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
5850    o pkg/ecco:
5851      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
5852      update all 4 lab_sea AD output.
5853    
5854    checkpoint62d (2010/03/22)
5855    o build_options:
5856      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
5857    o remove unbalanced quote (single or double) in commented line of source code
5858      (may cause some warning with some preprocessor/makedepend versions).
5859    o pkg/seaice:
5860      fix seaice_model.F for adjoint (gael) and update AD results of experiments
5861       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
5862    o testreport:
5863      add option '-runonly' (short: '-ro') to just do the run part (without make).
5864    o eesupp: remove JAM communication code (obsolete).
5865    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
5866      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
5867      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
5868      (update also the output).
5869    
5870    checkpoint62c (2010/03/02)
5871    o tools/build_options :
5872       move (some) old optfiles from build_options/ to build_options/unsupported/
5873    o model/src and pkg/exf
5874       surface relaxation -- separating data and data.exf options
5875       The point is to ensure that we specify the surface relaxation
5876       either in data or in data.exf (but not half and half) and to
5877       avoid an accidental relaxation to 0 (which happened if a time
5878       scale was specified but the file name was left empty)
5879    o model/src model/inc and pkg/mom_common
5880       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
5881       => addition to the viscosity field as computed by others schemes
5882    o tools/build_options:
5883      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
5884        but keep the former optfile for few weeks for smooth transition
5885    o pkg/ecco
5886      - allow user defined cost function contributions
5887         CPP: ALLOW_USERCOST_CONTRIBUTION
5888         USAGE: compute contributions in cost_usercost_all.F
5889      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
5890          the two options are complementary.
5891    o pkg/smooth
5892      - migration from contrib to the main repository
5893    
5894    checkpoint62b (2010/01/26)
5895    o pkg/monitor:
5896      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
5897        (in case someone forgot to update customized pieces of code)
5898    o nonHydrostatic:
5899      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
5900      - add a simple 2-D experiment (short_surf_wave) to test it.
5901    o pkg/icefront:
5902       adding the shell of, and the hooks to, a new package that
5903       will model melting and freezing of vertical glacier ice fronts
5904    o momentum:
5905      add diagnostics of momentum tendency from Hydrostatic pressure gradient
5906       (without surf.pressure term: would need a 2nd filling since implicit term).
5907    o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
5908      two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
5909      cannot deal with the former
5910    o cleaning:
5911      - remove all (except OpenAD) old TLM output from results_ad dirs.
5912      - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
5913      - comment out maskH definition (replaced by maskInC)
5914    o pkg/monitor:
5915      - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
5916        & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
5917    
5918    checkpoint62a (2010/01/15)
5919    o model/src:
5920      - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
5921    o pkg/diagnostics:
5922      - add optional level number diagnostics (i.e., level number to be define
5923        explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
5924      - strictly check for valid parser-code(10) ;
5925      - check if adding diag to the list from the right place.
5926    o pkg/longstep:
5927      - change parameters and fix tracer conservation with rstar/nonlinear free surface
5928    o diagnostics:
5929     - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
5930       S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
5931    o pkg/diagnostics:
5932     - Add option for writing vertical integral (sum of selected levels) of an output
5933        field instead of writing output field levels. Activate this option on a per
5934        output-file basis, by setting the 2nd character of fileflag to 'I'.
5935     - Add field-specific information relative to level integral in 3rd postion
5936        of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
5937        vertically (x level-thickness x hFac), "r"=same but without hFac.
5938    o do_the_model_io:
5939      - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
5940        in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
5941        writing pickups and stopping.
5942    o pkg/diagnostics (for now, only with mdsio):
5943      - write time information to meta file (and modify accordingly rdmds.m) :
5944        time-averaged diagnostics output: write starting and ending time of the
5945        time-averaging interval ; snap-shot diagnostics output remains unchanged;
5946    o pkg/timeave:
5947      - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
5948        always Nr), now assumed to be equal to number of levels of averaged field;
5949        only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
5950    o pkg/sbo:
5951      - fix ocean bottom pressure global-average & 2-D time-ave output (was
5952        neither initialised nor filled).
5953      - add starting iteration in suffix of global-average output file
5954        (to avoid over-writing the file after a restart)
5955      - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
5956    o time-average:
5957      - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
5958        (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
5959         ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
5960        this fix DIC_COST cumulative-time array (previously: bi,bj,k)
5961      - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
5962      - fix missing accumulation for pkg/opps.
5963      - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
5964         (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
5965      - fix initialisation of time-ave vars and do only full time-step increment
5966        (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
5967    o pkg/layers:
5968      - use standard RW pkg S/R to write the output
5969        and remove local write_fld version (which had a problem).
5970      - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
5971      - fix LAYERS_CALC argument list.
5972    o pkg/timeave:
5973      - store cumulative-time in a simple tiled array (drop the level index)
5974      - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
5975    o pkg/ocn,aim_compon_interf
5976      - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
5977    
5978    checkpoint62  (2009/12/23)
5979    o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
5980        (was not previously tested in any other exp.)
5981    o pkg/monitor:
5982      - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
5983        mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
5984        (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
5985      - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
5986      - change del2 calculation.
5987      - use interior masks (instead of maskH, <- to be remove).
5988      - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
5989    o mask & obcs:
5990      - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
5991      - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
5992        (called after packages_init_fixed)
5993    o pkg/obcs:
5994      - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
5995        Fixes bug in obcs+exf with nSx*nSy.GT.1
5996      - fix multi-tile handling in obcs balance code
5997    o nonHydrostatic:
5998      - Implement AB-3 for non-hydrostatic vertical momentum ;
5999        (change ordering of var. stored in pickup file when using NH)
6000      - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
6001      - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
6002        (in prep. for new NH free surface form).
6003    o pkg/obcs:
6004      add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
6005    o model/src:
6006      fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
6007    
6008    checkpoint61z (2009/12/01)
6009    o nonHydrostatic:
6010      Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
6011        a spurious source of energy in simple baroclinic adjusment test case.
6012      Update all non-hydrostatic exp output.
6013    o model/src (3-d solver):
6014      Change again 3-D solver free-surface RHS term when exactConserv=T:
6015        simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
6016        (which was not the case with previous formulation).
6017      To recover previous version, just reset "oldFreeSurfTerm" to previous value.
6018      Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
6019    o nonHydrostatic:
6020      - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
6021        for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
6022      - change 3-D solver to work with r* (for now, only with linear free-surf.)
6023      - add few debug diagnostics (cg3d_x, residual)
6024    o model/src:
6025      fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
6026        update output of exp. global_ocean.cs32x15.viscA4
6027    o update output of exp. global_ocean.cs32x15.icedyn after removing
6028      #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
6029    o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
6030    o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
6031      for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
6032    o model: add Christopher Wolfe's implemetation of the single reduction cg2d
6033      (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
6034      runtime flag useSRCGSolver. Modify verification experiment global_with_exf
6035      to test this code
6036    o pkg/cd_code:
6037      Change defaut D-grid time-stepping to get the same for D-grid momentum as for
6038       C-grid momentum. D-grid velocity used to be stepped forward in time with
6039       Adams-Bashforth only on surface pressure term. Tests show that using AB on
6040       D-grid coriolis term improves stability (as expected from CD-scheme paper).
6041      To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
6042      Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
6043       lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
6044       tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
6045      Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
6046           global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
6047    o pkg/obcs:
6048     - fix bug in initialisation (broken since Oct 1rst modification)
6049       for useOBCSprescribe without useEXF.
6050    
6051    checkpoint61y (2009/11/15)
6052    o pkg/seaice
6053     - change (once again) the discretization for the evp solver: rather than
6054       squaring the averages of strain rates, average the squares to give
6055       a better approximation to VP behavior (in simple test); this breaks
6056       verification experiments that use EVP (lab_sea and lab_sea.hb87)
6057        --> update outputs
6058    o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
6059      to improve vectorization of adjoint code on TARGET_NEC_SX
6060    o verification/vermix:
6061      - change vermix to a more "classical" 1d column with high vertical
6062        resolution, seasonal heat flux forcing and constant wind forcing
6063        --> update outputs
6064    o pkg/seaice
6065     - fix diagnostics of principal stress components for EVP
6066     - add optional diagnostics of non-linear convergence for LSOR solver
6067     - make maximum zeta a runtime parameter
6068    o model/src (3-d solver):
6069      Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
6070       which consisted in removing the Surf. Non-Hydrostatic pressure from the
6071       whole column and adding it to Eta (inspired from Casualli, 1999):
6072       Only affects 3-D solver initial guess and only if using ExactConserv,
6073       but tests did show a degradation of solver convergence. For this reason,
6074       decide to disable this piece of code.
6075       to recover previous version, just set zeroPsNH = exactConserv (line 78).
6076      Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
6077    o pkg/ggl90:
6078     - fix previous modif (unfortunatly has not been documented here).
6079    o pkg/seaice/autodiff:
6080     - add CPP flag to include clipping of zeta in EVP code;
6081       although clipping of zeta is not necessary for EVP and not recommended
6082       it was done by default, now clipping is disabled by default
6083     - modify computation and store zetaC/Z in seaice_evp for TAF
6084     - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
6085     - change seaice_calc_viscosities/strainrates for better
6086       vectorization after AD by TAF
6087     - rearrange common blocks in SEAICE.h once again for easier dumps of
6088       adjoint output, adjust adcommon.h and g_common.h
6089     - change flux form of default advection scheme for better vectorization
6090       of adjoint code
6091     - modify lab_sea/input.lsr to test the flux form of default advection
6092       scheme
6093    o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
6094      transition in checkpoint61r)
6095    
6096    checkpoint61x (2009/10/19)
6097    o adjoint: adding two new verification experiments
6098      * tutorial_global_biogeo: an online dic sensitivity experiment
6099        (work with G. Forget)
6100      * tutorial_dic_adjoffline: an offline dic sensitivity experiment
6101        (an update of the Dutkiewicz et al., 2006 paper)
6102      Both use the same CO2FLUX cost function, but different controls
6103      Gradient checks look good, but some recomp. could still be traightened out
6104      Should add xx_dic control variable to test at some point
6105    o model/src:
6106      add run-time parameters to check and/or mask initial Temp & Salt
6107    o pkg/ptracers:
6108      apply zonal filter (if used) to all passive tracers
6109    
6110    checkpoint61w (2009/10/12)
6111    o adjoint:
6112      * update and finish work on adjoint of dic package (G. Forget)
6113      * start adjoint of offline package
6114      * bug fix for cube-sphere TLM code (active_file_g.F)
6115    o tutorial_global_oce_optim:
6116      now tested with 4 tiles (change data.grdchk and update output_adm.txt)
6117      and add SIZE.h_mpi for MPI testing
6118    o pkg autodiff
6119     - fix bug in autodiff_restore
6120     - make genmake2 remove comments and empty lines from ad_input_code.f in
6121       order to reduce file size (new script file remove_comments_sed)
6122    o allows to specify vertical profile of vertical viscosity (viscArNr)
6123    o pkg autodiff
6124      autodiff_ini_model_io: comment out writing of grid information to netcdf
6125      files, because at this time the grid fields are a bunch of zeros
6126      (this is analogous to ini_mnc_vars.F)
6127    o pkg seaice/autodiff:
6128     left-over from removing the 3-time-level fields:
6129     - small rearrangement of common blocks (SEAICE.h)
6130     - fix field declaration in order to get meaningful output in
6131       adseaice.*.nc (adcommon.h)
6132    o pkg obcs:
6133     - go through NH code only if nonHydrostatic=T
6134     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
6135     - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
6136       => Update output of experiment seaice_obcs
6137     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
6138     - fix NH+Orlanski restart (add wvel OBC value in pickup file)
6139     - fix restart for useOBCSprescribe + useEXF
6140    o pkg ctrl
6141     - make obcs as control parameter work also with useSingleCPUio
6142     - replace a few sny and snx by Ny and Nx to be consistent with
6143       ctrl_set_globfld_x/yz.F
6144    o pkg seaice
6145     - re-introduce global field frWtrAtm for the case of
6146       ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
6147     - catch the case of an empty filename in seaice_cost_init_fixed.F
6148    o pkg ecco:
6149     - small bug fixes in the_main_loop
6150      . fix order of monitor arguments
6151      . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
6152      . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
6153        that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
6154     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
6155       imbalance diagnostics for wmean_h/sflux = 0
6156     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
6157     - catch the case of empty filenames in ecco_cost_init_fixed.F
6158       and ecco_readparms.F
6159     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
6160       to make this statement meaningfull in ecco_cost_weights.F
6161    o pkg zonal_filt:
6162      - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
6163      - when using rStar, filter uVel*hFacW instead of uVel
6164       (tested without topography: fix a Pb of growing instability with NLFS)
6165    o pkg/aim/thsice:
6166     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
6167      (works as SST restoring)
6168    o pkg/thsice:
6169     -add specific parameter for salt restoring in slab mixed-layer
6170       (by default equal to the temperature restoring)
6171    
6172    checkpoint61v (2009/09/21)
6173    o pkg/kpp:
6174     -add double diffusive contributions as a hack, turned off by default
6175      for now, and the code can be excluded with a CPP-flag
6176      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
6177     -add a verification experiments to "vermix" to test this code
6178    o pkg/mom_common:
6179      Move computation of length scales to mom_init_fixed.F (avoid recomputation
6180      at each time-steps*levels).
6181    o pkg/layers:
6182      Created a new package for computing volume fluxes in temperature or
6183      [not yet implemented] density layers, e.g. for calculating residual
6184      overturning circulations.
6185    o pkg/diagnostics:
6186      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
6187    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
6188    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
6189      To avoid mixing type (RS/RL) of input/output array argument,
6190      replace single mixed-type array with a pair from each type (RS/RL).
6191    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
6192      is now implemented for all pkgs (previously only done for the main pickup)
6193    
6194    checkpoint61u (2009/08/25)
6195    o pkg/obcs:
6196      - change OB?eta from _RS to _RL and put them into a separate commen block
6197      - add code to read OB?eta from a file via obcs_prescribe_read: the code
6198        compiles and does not destroy any other experiments, the data is read
6199        properly, but the code is not tested in actual applications
6200    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
6201      create a meaningful unit attribute for the time coordinate variable
6202    o pkg/ebm: add plenty of missing "_d 0" ;
6203       update results of experiment global_ocean_ebm (fwd + adjoint tests)
6204      Notes: several pieces of code only works for (very) specific set up
6205       (domain size, lat range, etc ...); should be documented & stop if one
6206       of those assumptions is not meet.
6207    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
6208       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
6209          and offline_exf_seaice (seaicetd + adjoint).
6210    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
6211       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
6212        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
6213    o few changes to pass when compiling with strick checking of arguments
6214       across S/R (allow to find few bugs in S/R calls).
6215    o pkg/seaice:
6216     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
6217       2d-fields, for slightly better performance
6218    
6219    checkpoint61t (2009/07/22)
6220    o pkg/seaice:
6221     - remove unused variables in seaice_evp
6222     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
6223    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
6224       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
6225       each processor opens a different file (a fix from Matt).
6226    o cg2d:
6227       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
6228       this reduces number of EXCH calls by 2 when using exch2.
6229       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
6230       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
6231    o pkg/thsice:
6232       add code for Near Infra-Red albedo (from Jeff)
6233       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
6234    o ini_model_io:
6235       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
6236       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
6237       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
6238    
6239    checkpoint61s (2009/06/30)
6240    o pkg/exch2 (exch2_rxN_cube*):
6241       remove last BARRIER (no need to synchronise after getting data from shared
6242       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
6243    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
6244      and generate new output (for the 2 tests) using default rotationPeriod.
6245    o pkg/exch2:
6246      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
6247        (was already the case with AUTODIFF_EXCH2 defined)
6248      - add bj in exch2 arrays and S/R.
6249      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
6250        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
6251    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
6252      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
6253        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
6254      - verification experiment natl_box.longstep
6255    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
6256      allow different versions of ifort (8 or 9) and different versions
6257       of mpi (mpich or mpich2) to be used with the same optfile.
6258      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
6259       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
6260    o pkg/seaice:
6261      fix previous modif (3-level field removed) for old-pickup reading
6262    
6263    checkpoint61r (2009/06/25)
6264    o pkg/seaice:
6265     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
6266      1. introduce fields for time step (N-1)
6267      2. do not use levels 2 and 3 anymore (but keep them)
6268      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
6269         includes changes to pkg/thsice/thsice_get_velocity.F,
6270         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
6271         pkg/obcs/obcs_apply_uvice.F.
6272     - completely remove code for leap-frog time stepping for second order
6273       advection
6274     - adjusted adjoint accordingly;
6275       gradient checks have improved by an order of magnitude!
6276    
6277    checkpoint61q (2009/06/22)
6278    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
6279     - the boundary conditions along open boundaries are unclear, because the
6280       associated masks are set to zero and are thus treated as closed when
6281       applying the slip-boundary conditions.
6282     - move initialisation of grid variables from seaice_init_varia to _fixed
6283    o adding doc/diags_changes.txt
6284    o model/src:
6285      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
6286       to avoid "_diags" naming if no relation to pkg/diagnostics.
6287      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
6288       file and only call PLOT_FIELD_XYZ if debugMode=T.
6289      remove few PLOT_FIELD_XY calls outside initialisation.
6290      remove few unnecessary BARRIER.
6291    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
6292      of salt_plume package in Southern Ocean
6293    o pkg/thsice:
6294     - fix hOceMxL in overlap (needed for sea-ice advection);
6295       update output of experiment global_ocean.cs32x15.icedyn.
6296    o pkg/seaice:
6297     - make the (placeholder-)tracer IceAge a little more meaningful
6298      by avoiding ridging of age due to convergent ice flow
6299     - add diagnostics for surface temperature, atmospheric and oceanic
6300       heat flux, and atmospheric and oceanic ice growth
6301    
6302    checkpoint61p (2009/06/10)
6303    o eesupp (global_max & global_sum):
6304     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
6305     - remove starting & endding barrier (no longer needed)
6306    o pkg/mdsio, writelocal:
6307       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
6308       (remove the STOP): uses shared buffer IO to store data from all threads
6309       and then let master-thread write nThreads tiles.
6310    o pkg/mdsio (read/write field):
6311     - tiled IO done in 1 piece (all levels at a time);
6312     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
6313     - multi-threaded: allow to read/write local (non-shared) array
6314       (was already working with singleCpuIO ; now works also without);
6315       => no longer needs barrier call after reading a file (added inside
6316       mds_read/write field).
6317     - move barrier calls outside gather/scatter_2d to mds_read/write_field
6318    o pkg/obcs/exf
6319      - exf_getffieldrec.F: add a few ". _d 0" and
6320                            add code to catch the case fldperiod = 0.  
6321      - obcs_precribe_read.F: change if statements so that they match
6322                              the variable type (_RL)
6323      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
6324        exf_iprec) as part of namelist EXF_NML_01
6325    o pkg/mdsio:
6326      - read/write tiled (local) files: read/write 1-level tile chunk at a time
6327        (instead of segment of length sNx); expected to speed up tiled IO.
6328    o pkg/exch2:
6329      - take buffer copy from/to array out of S/R exch2_send/recv into new
6330        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
6331        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
6332      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
6333      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
6334        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
6335        including Topology header file (and common blocks).
6336      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
6337        remove 2nd exch call in exch2_s3d_rx (no longer needed).
6338      - document S/R arg. list (+ update some comments)
6339    o pkg/seaice:
6340      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
6341        temperature and humidity over sea ice based on climatological values.
6342      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
6343        of LSR (this change is expected to change the results slightly because now
6344        it uses slightly difference moduli from the second last LSR solution, but
6345        that is more consistent with the stress computations; this part of the code
6346        is not tested in the verification experiments)
6347      - fix diagnostics for flux of ice in case of B-grid
6348      - turn strain rates eij and press into global fields within global
6349        common block in SEAICE.h for more straighforward diagnostics
6350      - fix diagnostics for principal stress components, press, zeta, eta
6351        to give something meaning full
6352    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
6353      new output (all 4 tests) using default rotationPeriod.
6354    o pkg KPP:
6355      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
6356      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
6357        and normal grid from 1 to Nr)
6358    o Fix computations of L4rdt in mom_calc_visc.F
6359    o eesupp:
6360      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
6361      should be called before a "stop" if we know that all process are going
6362      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
6363    
6364    checkpoint61o (2009/05/26)
6365    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
6366    o model/src/ini_curvilinear_grid.F:
6367       compute angleSin/CosC when they are not read from a file
6368    o pkg/seaice:
6369       add pseudo time stepping for LSOR
6370    o pkg/exch2:
6371       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
6372    o pkg/seaice:
6373       Adding separate sea ice albedo, drag coefficients, and HO in Southern
6374       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
6375    o SingleCpuIO:
6376       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
6377    o pkg/seaice:
6378       put exchanged variable in (local) common block for MPI+Multi-Threads
6379       to work (necessary with exch1, and for now with exch2 too).
6380    o verification: to get more experiments tested with mpi, mth and mpi+mth,
6381      change tiling of:
6382       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
6383       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
6384      update output of exp:
6385       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
6386       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
6387      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
6388                       (note: output.txt generated on faulks using only 1 tile)
6389    o eesupp & mdsio (SingleCpuIO):
6390     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
6391       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
6392       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
6393     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
6394     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
6395       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
6396    o pkg/exch2:
6397     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
6398       read parameter file "data.exch2" if it exists; otherwise try default regular
6399       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
6400     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
6401       with new code (not to be used, just as a backup solution).
6402     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
6403       in utils/exch2/input.
6404    
6405    checkpoint61n (2009/05/12)
6406    o eesupp & mdsio (SingleCpuIO):
6407      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
6408        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
6409        receive real*4 array (instead of real*8) to read/write 32.bit files.
6410        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
6411         and remove new mapping S/R)
6412    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
6413      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
6414        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
6415        when using exch2. Add S/R to map global io-buffer to global model array.
6416      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
6417    
6418    checkpoint61m (2009/04/29)
6419    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
6420      and add 3 other S/R for other types (R4,R8,RS).
6421      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
6422    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
6423     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
6424     - reduce number of macro definitions (keep only those which are used);
6425       can always call directly the corrresponding S/R if needed.
6426     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
6427       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
6428     Fixed wrong type of arg in:
6429       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
6430       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
6431     To fix: global_sum of var in common block is wrong (multi-threaded) in:
6432       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
6433     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
6434    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
6435      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
6436    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
6437    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
6438      edges are closed (zero depth); might happen with "blank tiles";
6439      for now, disabled if using OBCS.
6440    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
6441      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
6442    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
6443      to reduce length of 1.D array print in STDOUT.
6444    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
6445      + use 48 tiles (16x8): this will allow to test "blank tiles".
6446    o start to test MPI + multi-threaded (change testreport to skip tests
6447      where number of tiles do not match).
6448    o genmake2: add option "-omp" to turn on Open-MP ;
6449      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
6450    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
6451      and keep the original tile numbering. Note: compatible with old
6452      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
6453    
6454    checkpoint61l (2009/04/07)
6455    o Overlaps had been forgotten in calculating ijk keys : fixed
6456    o fix cyrus makedepend for gcc 4.4
6457    o experiment fizhi-cs-aqualev20:
6458      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
6459      and generate new output. Note: new output is much closer to the old
6460      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
6461      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
6462    o pkg/fizhi:
6463     - change to avoid indices going deliberately over array-bounds
6464     - remove unnecessary MPI stuff
6465     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
6466     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
6467       does not go over array-bounds and therefore returns reliable output.
6468     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
6469       this S/R has 4 output arguments, which are used inside "get_alarm";
6470       when it is called with the same variable "ndum" in place of several
6471       output arguments, this produces weird side effect inside "get_alarm"
6472      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
6473       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
6474       address) and produces error.
6475    o tools/gemake2: (March 27-29 2009)
6476      with option "-mpi": link *_mpi files from "MODS" dir (this is what
6477      testreport does).
6478    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
6479    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
6480       update lab_sea.lsr & lab_sea.salt_plume results
6481    o pkg/seaice:
6482      Major overhaul of the LSOR solver: change discretization from original
6483      finite differences to finite volume. The old routine is still in the
6484      file seaice_lsr.F and can be turned on with the CPP-flag
6485      SEAICE_OLD_AND_BAD_DISCRETIZATION
6486      Along with this change, the discretization of the strain rates is changed.
6487      The same flag turns on the old discretization in seaice_calc_strainrates.F
6488      All verification experiments with seaice are affected (except for
6489      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
6490      results by setting the above flag.
6491      Further changes involve changes in defaults:
6492      - ALLOW_FLOODING is defined and turned on by default
6493      - SEAICEadvSnow = .true. is now the default
6494      - SEAICEadvSalt = .true. is now the default
6495      - SEAICEadvAge  = .true. is now the default
6496      - SEAICE_clipVelocities  = .false. is now the default
6497                                         (as per J. Zhang's recommendation)
6498      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
6499        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
6500      - seaice_growth: replace computation of UG by a simple copy from wspeed
6501    
6502    checkpoint61k (2009/03/18)
6503    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
6504      seaice_lsr: fixed a few metric terms,
6505                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
6506                  add more debugging diagnostics
6507      seaice_evp: removed superfluous many metric terms of FV discretization
6508                  of stress divergence
6509                  affects lab_sea, lab_sea.hb87
6510      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
6511                  of stress divergence for non-evp solver
6512                  (this part is not tested anywhere)
6513      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
6514                  they were effectively only half slip
6515                  affects lab_sea.hb87
6516      updated all relevant verification experiments (except lab_sea//output_adm.txt
6517        which was left over, but fails at level 7 & 6)
6518    
6519    checkpoint61j (2009/03/17)
6520    o pkg/seaice: turn a few hard wired parameters into run time parameters
6521    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
6522      time in seconds as promised by the usints in seaice_monitor and exf_monitor
6523    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
6524      that are not cubed-sphere grids
6525    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
6526    o pkg/ctrl:
6527      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
6528    o non-hydrostatic (calc_gw.F):
6529      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
6530      update output of exp. global_ocean.cs32x15.viscA4
6531    o remove backward compatibility for thetaMin,phiMin
6532      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
6533    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
6534      interpolated wind field not only for curvilineargrid=.true., but also
6535      for a rotated grid (rotateGrid=.true.)
6536    o pkg/exf: add capability to bypass interpolation for runoff
6537      by setting yet another CPP-flag
6538    o eesupp/src, B-grid exchange:
6539      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
6540    o autodiff
6541      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
6542      allows to switch to single-prec common blocks;
6543      corresponding switch occurs in tamc.h, integer isbyte
6544      TAF store directivs "byte" and "kind" seem equivalent;
6545      Most tamc.h have been updated correspondingly.
6546    
6547    checkpoint61i (2009/02/13)
6548    o autodiff:
6549      fix autodiff_sore/_restore indices for obcs
6550      (spotted by I. Hoteit, M. Mazloff)
6551    o pkg/autodiff, pkg/ctrl:
6552      Add flag to reduce all tapelev I/O to single-prec.
6553      In data.ctrl set
6554        doSinglePrecTapelev = .TRUE.
6555    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
6556      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
6557    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
6558      real fresh water flux (not yet)
6559    o pkg/mdsio & rw:
6560     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
6561     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
6562    o pkg/flt:
6563     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
6564       init_fixed & ini_varia.
6565     - clean-up & simplify linear interpolation S/R:
6566       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
6567     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
6568     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
6569     - add vert. coordinate & horiz. indices to output files.
6570     - change vertical position in initial condition, from index to depth [m].
6571     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
6572       (easier to get to a curvilinear grid) ; delX,delY no longer used.
6573    o pkg/ggl90: a few modifications:
6574     - fix bottom boundary condition, and interpolation of KappaE
6575       near top and bottom
6576     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
6577     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
6578     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
6579    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
6580      (maintain temporary backward compatibility, until next checkpoint)
6581    
6582    checkpoint61h (2009/01/27)
6583    o pkg/diagnostics with "periodic averaging diagnostics":
6584      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
6585    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
6586    o pkg/obcs: fix loop ranges for balancing code
6587    o pkg/flt:
6588     - improve criteria for finding which tile owns a float.
6589     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
6590    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
6591      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
6592      with ocean biogeo)
6593    o pkg/flt:
6594     - do some cleaning and fix the restart ;
6595     - add output.txt in flt_example/results to get this pkg tested.
6596    o genmake2: add an EXTENDED_SRC option and flag.
6597       for now, cannot be turned on on command line (only through genmake_local)
6598    o pkg/mdsio: read/write vector:
6599     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
6600     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
6601       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
6602     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
6603      (drop to 4 digits matching for grad). But this test does not look very
6604      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
6605    
6606    checkpoint61g (2008/12/29)
6607    o pkg/flt:
6608      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
6609       + make OPTIONS file more standard.
6610      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
6611      - fix _BYTESWAPIO CPP-Flag
6612      - standard reading of file-parameter "data.flt"
6613      - fix argument list of S/R FLT_RESTART
6614      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
6615    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
6616    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
6617      a still unfixed compiler/optimization bug
6618    
6619    checkpoint61f (2008/11/21)
6620    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
6621      update results of global_ocean.cs32x15.icedyn test.
6622    o move getcon.F from model/src to pkg/fizhi.
6623    o pkg/exf: add parameter for extrapolation of temp up to the surface
6624       and option to prevent negative evap (in bulk_largeyeager04 only).
6625    o Prather Advection scheme: fix tracer conservation for divergent flow
6626      (e.g., when using NonLin Free-Surface).
6627    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
6628    o gmredi (Visbeck-variable-K):
6629     - add more parameters to Visbeck-variable-K.
6630     - use a 5 points average for dSigmaR in Visbeck-K calculation
6631       (more "homogenous": same stencil and same weights as in dSigmaH)
6632     - update output of ideal_2D_oce experiment.
6633    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
6634      (#undef REAL4_IS_SLOW)
6635     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
6636       coordinate variable
6637     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
6638       (surface forcing fields), removes some of the functionality
6639     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
6640     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
6641       probably not all: copy _RS surface flux fields to RL field before
6642       calling DIAGNOSTICS_FILL
6643     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
6644       real*4 (CALL EXCH_*_RS) versions.
6645     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
6646       (generate new output).
6647    
6648    checkpoint61e (2008/10/23)
6649    o gmredi (Visbeck-variable-K):
6650      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
6651      - change computation of Visbeck-K where Slope > Smax :        
6652        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
6653        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
6654    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
6655      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
6656    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
6657    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
6658      does not become too large (to avoid precision problems in implicit-diffusion
6659      solver); update ideal_2D_oce output.
6660    o pkg ggl90:
6661      - in ggl90_cal.F: compute only one set of visc/diff, used to
6662        step forward TKE/T/S/momentum
6663      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
6664        have Prandlt =1)
6665    o gmredi (fm07):
6666      - add lower limit on Transition layer thickness + lower limit on 1/lambda
6667      - allow to set few more params from data.gmredi
6668    o pkg ggl90:
6669          - add missing sqrt(2) factor in computation of mixing length
6670            scale in ggl90_calc.F
6671            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
6672    
6673    checkpoint61d (2008/09/25)
6674    o adjoint modifs
6675      - adapt to new field rhoInSitu
6676      - allow to revert from StoreDynVars2D, StoreDynVars3D
6677        to individual fields
6678        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
6679    o store 3-D (in-situ) density in commom block (DYNVARS.h)
6680     - save 1 rho computation.
6681     - no longer modify T & S inland when using down_slope pkg.
6682    o gad_som : allow to switch to SOM advection for T & S without corresponding
6683      pickup files (using new S/R: MDS_CHECK4FILE).
6684    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
6685      (for useSingleCpuIO to work in multi-threaded)
6686    o pkg/shelfice:
6687     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
6688       with SHELFICEtopoFile in data.shelfice
6689     - move code for reading ice shelf topography and modifying hFacC into separate
6690       subroutines of the shelfice package
6691     - separate initialisation of "fixed" and "variable" variables
6692     - kTopC is not (yet) replaced by kSurfC, although this is possible
6693    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
6694    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
6695      and rename:
6696      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
6697      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
6698    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
6699    
6700    checkpoint61c (2008/08/30)
6701    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
6702      to add mass source/sink of fluid in the interior (3-D generalisation
6703      of oceanic real-fresh water flux).
6704    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
6705    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
6706    o new pkg: down_slope
6707      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
6708      - presently, modify T & S inland (dwnslp_calc_rho.F).
6709        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
6710      - implementation for ocean in P-coords not tested.
6711      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
6712    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
6713      (to facilitate conversion of oceanic pkg to p-coordinate).
6714    o change FIND_RHO to FIND_RHO_2D :
6715      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
6716    o new pkg: cheapaml
6717    
6718    checkpoint61b (2008/08/05)
6719    o exch2:
6720      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
6721      - no longer depend on the order sequence (N,S,E,W).
6722      - 3rd exchange no longer needed (tested with 24 tiles).
6723      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
6724      - exch_UV_A-grid readily available (but not yet tested).
6725      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
6726      (both are no longer needed) in exch_uv: no effect in forward run; but
6727       get truncation error differences with adjoint exch.
6728    o exch2:
6729     - change index-bounds storage (moved from target to local tile,
6730       more intuitive this way) ; rename/remove some variables.
6731     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
6732    
6733    checkpoint61a (2008/07/29)
6734    o exch2/matlab-topology-generator:
6735      fix bug in index bounds for N-S internal exchange (hard to tell if this
6736      had any effect on the solution).
6737    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
6738      is exceeded
6739    o testreport: modify syntax of awk, so that it works also with
6740      awk, and not only with nawk and gawk
6741    
6742    checkpoint61 (2008/06/24)
6743    o autodiff
6744      Change default for TAF usage by removing argument '-nonew_arg'
6745      This changes TAF subroutine argument list (ordering of active var.)
6746      Omission of this flag leads to incompatibility w.r.t. TAMC
6747      To restore TAMC-compatibility, need following modifs:
6748      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
6749      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
6750      Tested TAF version is 1.9.22
6751      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
6752    
6753    checkpoint60 (2008/06/19)
6754    --->>> This is the last checkpoint for which generating the adjoint
6755    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
6756    --->>> by default.
6757    --->>> Future checkpoints will ommit this flag by default.
6758    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
6759    o pkg/grdchk: Add gradient check to etan0 perturbations.
6760    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
6761    o pkg/autodiff: more flexibility in zeroadj.
6762      model/src: modifying do_oceanic_phys.F accordingly.
6763    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
6764    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
6765      special setup of gmredi for which the adjoint is stable
6766      enough for parameter optimization.
6767    o bridging the gap between eddy stress and GM.
6768      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
6769          along with a change in CPP option (now ALLOW_EDDYPSI).
6770      -> when using GM w/ GM_AdvForm:
6771          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
6772          is applied either in the tracer Eq. or in momentum Eq.
6773          depending on data.gmredi (intro. GM_InMomAsStress).
6774      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
6775      The key modifications are in model/src/taueddy_external_forcing.F
6776      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
6777    
6778    checkpoint59r (2008/05/29)
6779    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
6780      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
6781      fix option to read coriolis(@ cell-corner) from files with CS-grid.
6782    o pkg/mnc: add some attributes to standard 1D-coordinate variables
6783    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
6784      mass points, when using mnc for output
6785      - add runtime parameter (missing_value, missing_value_int) to override
6786        default (which is the value of getcon('UNDEF'))
6787    o pkg/mnc: prepare mnc for the actual use of missing values with the
6788      diagnostics package: small fix in mnc_cw_readwrite.template and more
6789      initialisation of never used fields
6790      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
6791      versions
6792    o pkg/thsice/thsice_ini_vars.F added default initial values so that
6793      thermodynamics sea ice solver does not blow up when some initial fields
6794      are missing.
6795    o move from external_forcing_surf.F to ini_forcing.F
6796      the p-coord. hack consisting in using pLoad to set phi0surf ;
6797      update output of tutorial_global_oce_in_p (affected @ truncation level).
6798    o Freshen up a bit hs94.1x64x5, notably:
6799      remove rotationPeriod and tRef=5*0. (adjoint only), and add
6800      exactConserv=.TRUE.
6801    o pkg/generic_advdiff:
6802      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
6803      applies to files where Temperature & Salinity 2nd Order moments are used.
6804    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
6805      this uses a dynamically allocated internal state data structure
6806      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
6807      and requires a fortran 90 compiler
6808    
6809    checkpoint59q (2008/05/06)
6810    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
6811       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
6812    o Refresh tutorial_global_oce_biogeo, notably:
6813      - change bathymetry (put back seamounts in ACC, use hFacs)
6814      - change EOS (POLY3 --> JMD95Z)
6815      - use Bryan-Lewis vertical diffusivity
6816      - use multidimensional advection
6817      - remove old virtual virtual in dic pkg, now done through ptracer pkg
6818      - change a couple of parameters in dic pkg
6819    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
6820    o pkg/obcs: change default to OBCSfixTopo = .true.,
6821      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
6822      - replace "debugMode" with "debugLevel .GE. debLevB"
6823    o implementation of TAF directives for gchem,cfc,dic
6824    o remove "exp5" (replaced by tutorial_deep_convection).
6825    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
6826      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
6827      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
6828      --> changes results in exp4, seaice_obcs
6829    o tutorial_deep_convection :
6830      update the set-up and increase resolution and domain size ; start
6831      from pseudo initial conditions = output at t=120mn in order to see
6832      something happening when running testreport.
6833    o pkg/seaice: add os7mp as an advection scheme
6834                  add check for advection schemes
6835                  add a flag for restoring T and S underneath sea ice
6836    o pkg/my82: add netcdf-support and diagnostics
6837    o thsice pkg:
6838      - Now hsMax limits snow height by turning it into ice following
6839        flooding scheme (and now conserving energy)
6840      - Slight rewriting of the formula in thsice_calc_thick.F
6841      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
6842      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
6843    
6844    checkpoint59p (2008/04/10)
6845    o gchem / dic / cfc :
6846      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
6847      - add new parameter files: "data.dic" & "data.cfc" ;
6848      - various re-arrangement in initialisation & header file ;
6849      - fix tutorial_global_oce_biogeo for multi-threaded test.
6850    o pkg/dic: test for "pickup_dic" file when restarting ;
6851      if no pickup-file, can restart with a re-initialised pH (same as it did
6852      before) providing pickupStrictlyMatch is set to False.
6853    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
6854      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
6855    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
6856      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
6857    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
6858     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
6859       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
6860    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
6861       scheme to use for vorticty-term ;
6862     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
6863       (with default selectVortScheme, return to original discretisation)
6864     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
6865    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
6866    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
6867      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
6868      also fix diagnostics VISCAHW & VISCA4W.
6869    
6870    checkpoint59o (2008/03/07)
6871    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
6872    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
6873      move a few statemens out the main loop into separate loops
6874    o pkg/shelfice:
6875      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
6876        (kg/m^2/s), does not break tests, because in verification/isomip,
6877        rhoConstFresh=rhoConst (by accident)
6878      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
6879      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
6880        new file model/src/seawater.F, so that they are available for all pkgs.
6881      - convert potential temperature into in-situ temperature. This changes the
6882        isomip tests => update tests
6883    o add a flag writePickupAtEnd (default=true) to be able to suppress
6884      writing a pickup at the last timestep
6885    o tools/mpack-1.6 :
6886      - disable automake (not working) and autoconf (not needed).
6887      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
6888        also cleaner with much less compilation warnings.
6889    o pkg/profiles:
6890      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
6891      (for "less than 32 characters name" compiler requirement)
6892    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
6893      conditions that have a different sampling frequency than S/T/U/V obcs
6894    o pkg/diagnostics (stats-diags):
6895      - fix global Min/Max in case 1 processor get only empty tiles
6896    o genmake2: replace (4 times)
6897         make genmake_tc_1.o >> genmake_warnings 2>&1
6898      with
6899         COMM="$CC $CFLAGS -c genmake_tc_1.c"
6900         echo $COMM >> genmake_warnings
6901         $COMM >> genmake_warnings 2>&1
6902      to make genmake2 always see the value of CC as specified in the optfile.
6903    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
6904      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
6905      - modify verification advect_cs test to test SOM-advection on CS-grid.
6906    o pkg/ctrl:
6907      - Rewrite of ctrl_map_ini_ecco.F,
6908        introducing a generic routine (ctrl_map_ini_gen.F).
6909      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
6910    
6911    checkpoint59n (2008/02/09)
6912    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
6913      number in dedicate array "hdiag":
6914      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
6915        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
6916      - many small changes (integer format) for large number of diagnostics
6917      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
6918        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
6919    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
6920      usingSphericalGrid, this allows to define the rotated grid coordinates
6921      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
6922      geographical coordinates according to the inverse of the rotation defined
6923      by the Euler angles, so that Coriolis parameter and online-interpolation by
6924      exf works with the geographical coordinates on XC/YC/XG/YG.
6925      Naturally, this feature does not work with all packages, so some
6926      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
6927      profiles), because there the coordinates are assumed to be regular
6928      spherical grid coordinates.
6929    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
6930      - introduce isopycnal diffusion coefficient control.
6931    o tools/adjoint_options:
6932      - additional control vector components.
6933    o pkg/mnc: have mnc create marginally meaning full coordinate variables
6934      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
6935    o pkg/mypackage:
6936      - add example of read/write pickup for state-var ;
6937      - add entry points to the main code for state-vars diags & write-pickup.
6938    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
6939      transitions for useExfYearlyFields
6940      - add new subroutine that determines the file to read from for
6941        use*YearlyFields = .TRUE. and .FALSE.
6942      - add a verification experiment to global_with_exf that tests
6943        useExfYearlyFields with USE_EXF_INTERPOLATION defined
6944    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
6945      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
6946      subroutines (which could be generated from a template, because they are
6947      almost identical), for now they are included in obcs_prescribe_read.F for
6948      simplicity
6949    o pkg/exf:
6950      - add a little more diagnostic to exf_interp_read (in analogy to
6951        mds_read_field, can be turned off with debugLevel < debugLevA=1)
6952      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
6953        ugly but fast by unrolling short inner loops, inserting a unroll=8
6954        directive in routine lagran, and splitting a loop and making do while the
6955        outermost loop (the latter requires the intoduction of index arrays)
6956    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
6957    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
6958      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
6959    o verification/seaice_obcs: updated for restart test and latest options
6960    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
6961      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
6962      for now this is only available for the C-grid code and also within
6963      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
6964    
6965    checkpoint59m (2008/01/14)
6966    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
6967      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
6968    o gad_som : fix flux output (& diagnostics) to have same units as other  
6969      advection scheme fluxes (was previously multiplied by deltaT).  
6970    o added verification/seaice_obcs both to test seaice open boundaries
6971      and to provide an example matlab scrpt for generating them
6972    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
6973    o pkg/salt_plume: clean up salt_plume_frac.F to
6974      remove redundancy in PlumeMethod 1 and 4
6975    o pkg/kpp: added saltplume diagnostics
6976    o pkg/obcs and pkg/seaice:
6977      - do not set uice and vice to zero when OB*icefile are unspecified
6978      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
6979      - moved seaice tracer obcs after call to seaice_growth
6980    o pkg/salt_plume: added various options for salt plume depth
6981      criterion and for vertical distribution of the salt
6982    
6983    checkpoint59l (2007/12/18)
6984    o pkg/ptracers: new version of ptracers pickup:
6985      read meta file and write only fields which are needed to restart.
6986      ( same logic as main pickup file ; also using pickupStrictlyMatch )
6987    o pkg/seaice:
6988      - add timescale for melting due to warm mixed layer as a means of
6989        setting SEAICE_availHeatFrac more conveniently
6990      - add a CPP-flag/runtime parameter check for flooding algorithm
6991      - reformulated availHeat in seaice_growth.F to be independent of AREA
6992    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
6993      unit changes
6994    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
6995    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
6996      SX vector computer.
6997    o pkg/seaice:
6998      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
6999        seaice forcing fields can now be read only through pkg/exf
7000      - removed some unused halos
7001    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
7002    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
7003      or U/VICE from U/VWIND before computing U/VSTRESS
7004    
7005    checkpoint59k (2007/11/30)
7006    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
7007      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
7008    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
7009      all experiments pass when compile with un-initialised var. checking option.
7010    o added pkg/salt_plume
7011    o script to test restart (for now, in MITgcm_contrib/jmc_script)
7012    o pkg/seaice: new read/write pickup version.
7013      read meta file and write only fields which are needed to restart.
7014      ( same logic as main pickup file ; also using pickupStrictlyMatch )
7015    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
7016    o lab_sea.hb87: modify the domain & update output.hb87.txt :
7017      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
7018      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
7019      process. Fixed here by closing the domain at the Northern boundary.
7020    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
7021    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
7022      a set of consecutive levels in/from a 3-D array.
7023    o pkg/ptracers:
7024      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
7025      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
7026    
7027    checkpoint59j (2007/11/09)
7028    o in pkgs: dic, obcs, offline, rbcs:
7029      standard way to compute coeff. for time interpolation between 2 time reccords
7030      which retains full precision (& make results less dependent on compiler).
7031      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
7032    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
7033      packages instead of reading ice cover and wind speed separately
7034    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
7035     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
7036      to allow to compile customized code before the update)
7037    o cleaning-up:
7038      - fix CPP instruction syntax in pkg/obcs
7039      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
7040        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
7041      - fix some threads issue in IO parts.
7042    o pkg/dic:
7043      - add tons of "_d 0" (--> much better testreports !)
7044       and then update outputs of tutorial_global_oce_biogeo
7045    o pkg/mom_fluxform:
7046      add a special version of momentum advection intended to conserve momentum
7047      next to a bathymetry step or a coastline edge. (default = off = #undef)
7048    o new read/write pickup version:
7049      - for now, only implemented for main (mdsio) pickup file.
7050      - write out only what is needed to restart; merge pickup_nh , pickup_ph
7051        and main pickup together.
7052      - read meta file; read only what is needed to restart; stop if a field
7053        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
7054        if it make sense (even if the restart is not perfect).
7055      - if no meta file, assume that pickup to read corresponds exactly to
7056        a pickup that would currently be written.
7057      - read pickup written in the old format (until checkpoint59i) if it
7058        recognizes an old meta file (no field-list).
7059      - add a meta file in exp. which starts from a pickup: 2 cases:
7060        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
7061         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
7062        b) a meta file describing the content of the associated pickup file
7063         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
7064    o pkg/mdsio & pkg/rw:
7065      - new routine to read a meta file ; new set of routine to read
7066        Multiple-fields file (with meta file).
7067    o added open boundary conditions capability for seaice
7068        HSNOW, HSALT, UICE, and VICE
7069    
7070    checkpoint59i (2007/10/21)
7071    o adjoint:
7072      * fix multiDimAdvection adjoint
7073        (partial recomputation problem by TAF for fVerT(:,:,kDown)
7074        and comlev1 size definition (maxpass vs. max. number of tracers)
7075      * verification/global_ocean.90x45x15 adjoint now tests
7076        NLFS and multiDimAdvection using DST3 (=30)
7077      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
7078    o pkg/kpp: add "_d 0" to real constant (if missing);
7079      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
7080      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
7081    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
7082      for internal parameters related to restart process (formerly from PARAMS.h)
7083      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
7084    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
7085      as argument. (only atm2d & obcs write_pickup have not yet been updated)
7086    o pkg/monitor:
7087      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
7088      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
7089      - account for deep Atmosphere factor and density factor (anelastic)
7090    o added open boundary conditions capability for seaice HEFF and AREA
7091    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
7092      thermodynamics
7093      - requires a little reorganization, which affects the testreport results
7094        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
7095        so that now the conservative form is tested
7096      - add a few comments
7097    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
7098    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
7099    o add new diagnostics to seaice: advective, diffusive fluxes (only for
7100      multidim-advection, for scheme 2 they are not filled) and transports,
7101      thermodynamic growth rates
7102    o change units of EmPmR (inside the code, + within coupling interface)
7103      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
7104      Affects results @ truncation level (cg2d match) and update output of
7105       experiments: lab_sea(6), global_ocean.90x40x15(10),
7106      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
7107      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
7108      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
7109      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
7110    
7111    checkpoint59h (2007/09/29)
7112    o pkg/exf:
7113      - improve vectorization by moving if-statement out of loops in
7114        exf_mapfields, exf_radiation
7115      - exf_bulkformulae.F: introduce 2D fields and vectorize code
7116    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
7117    o testreport:
7118      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
7119        monitor & update offline_exf_seaice exp. output.
7120      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
7121    o pkg/seaice:
7122      - bug fix in the evp solver: boundary conditions were affected be
7123        masking of zMax/zMin (changes results)
7124      - minor bug fix in boundary conditions in seaice_calc_strainrates
7125        (changes results for no_slip)
7126      - seaice_lsr.F: make interpolation of eta dependent on boundaries
7127      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
7128      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
7129        stress formulation and no-slip boundary conditions
7130    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
7131      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
7132    o pkg/seaice: a first HSALT time stepping equation has been checked in
7133    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
7134      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
7135      without requiring DO-IF statements
7136    o pkg/thsice:
7137      use continuous power-law function for partition of energy between lateral
7138      melting/freezing and thinning/thickening ; old code using step function
7139      still available with #undef THSICE_FRACEN_POWERLAW
7140      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
7141    o testreport: change AD testing : check against results/output_adm.txt
7142      using same scripts as for forward test.
7143    
7144    checkpoint59g (2007/09/17)
7145    o adjoint testing: in preparation for changing testreport:
7146      - output format: cost and grad written on separated lines
7147      - ad output results in directory "results" (instead of "results_ad")
7148    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
7149    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
7150    o pkg/ecco: allow user defined cost function contributions
7151    o testreport:
7152      Allow to choose (per experiment) the list of tested output variables
7153       and the main variable (used to issue a pass/FAIL ) ;
7154      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
7155      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
7156      Also modify printing of summary:
7157       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
7158       b) echo the list of tested variables in the individual summary.txt of
7159          each experiment.
7160    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
7161      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
7162      (but still depend on the tile decompostion of the domain).
7163    o pkg/seaice: change a discretization detail to make the B-grid code
7164      "more symmetric". This change is likely to remove all "ridges/leads" that
7165      where quasi-aligned with the grid in B-grid solutions. It may also be
7166      the solution to the stress coupling issues with the B-grid.
7167    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
7168      remove .cvsignore from input dir. (since testreport no longer run here).
7169    o pkg/thsice:
7170     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
7171     - fix reshaping of sea-ice just after advection:
7172       melt all the ice only if ice-volume is too small.
7173     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
7174       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
7175     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
7176    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
7177      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
7178    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
7179      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
7180      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
7181      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
7182      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
7183      -> update output.txt
7184    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
7185     this affects truncation error: -> update output.txt of exp:
7186      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
7187      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
7188    
7189    checkpoint59f (2007/08/21)
7190    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
7191    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
7192      a bounded range (in forward mode)
7193    o pkg/ecco, ctrl, autodiff and mom_common:
7194     internal parameter controls, completements of implementations
7195    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
7196    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
7197      (not seem any difference in testing results).
7198    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
7199       at face corners.
7200    o pkg/generic_advdiff:
7201     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
7202      loop range indices for computing vertical advection tendency
7203      and do the calculation in the interior only (no overlap) ;
7204      for now, only implemented for SOM advection (to save CPU time).
7205     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
7206    o exch2 adjoint
7207      First set of changes:
7208      - add exch2 hand-written adjoint templates
7209      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
7210        This will require cleanup in pkg/autodiff/*.F
7211        (changed routines currently kept separate in verif. code/)
7212      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
7213        that used to hide exch2 or cubed-sphere specific code
7214        (commented via 'cph-exch2')
7215    o pkg/seaice
7216      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
7217    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
7218       output of global_ocean.cs32x15.thsice .
7219    
7220    checkpoint59e (2007/07/26)
7221    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
7222      for B-grid vector (not yet tested) and C-grid vector (<- only used
7223      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
7224    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
7225      (#ifdef ALLOW_SALT_PLUME)
7226    o gather_2d/scatter_2d: removed halo regions
7227    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
7228      scheme and the corresponding test case (under front_relax dir). For now,
7229      only available with Skew-flux form and not yet tested in realistic set-up.
7230      adjoint: store directives updated, but gradient checks deteriorated,
7231      so maybe GM/Redi adjoint is now broken.
7232    o seaice adjoint
7233      * add AREA, HEFF, HSNOW as control variable
7234        (should not change lab_sea results)
7235      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
7236    o pkg/seaice:
7237      * added computation of saltFlux in seaice_growth;
7238        For time being, sea ice salinity is assumed constant
7239        contribution of snow flooding to freshening of sea ice is neglected.
7240        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
7241        defaults to 0.0 in order to maintain backward compatibility.
7242        Typical values for SEAICE_salinity are 4 to 10 g/kg.
7243      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
7244      * added SEAICE_availHeatFrac, which specifies fraction of surface level
7245        heat content used to melt or grow ice
7246      * commented out cap of HICE: it helps keep ice thinner
7247      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
7248      * applied OBCS T/S mask to HEFFM sea ice mask
7249    
7250    checkpoint59d (2007/06/21)
7251    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
7252     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
7253     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
7254    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
7255     and change default value of parameter "GM_Small_Number";
7256     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
7257       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
7258       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
7259    o pkg/ecco: cost function when applying pkg/smooth to controls
7260    o pkg/ctrl: add forcingPrecond run time parameter
7261    o pkg/seaice:
7262     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
7263     - fix bug in metric terms of u-equation in LSR solver (implicit part),
7264       changes verification/lab_sea
7265     - rearrange implicit part of u-equation in LSR solver to make it easier to
7266       read, understand, and debug. This causes changes at the truncation level.
7267     - fix (serious) bug in the boundary conditions (sign error in the implicit
7268       part) of the LSR solver. Changes all LSR results.
7269     - fixed problem with HSNOW initialization to avoid thick snow when AREA
7270       is initilized with small values - does not change lab_sea results.
7271     - added HsnowFile initialization capability
7272    o pkg/smooth: addition to model/src and pkg/ctrl so allow
7273     initialization of pkg/smooth and application to control vector
7274    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
7275    o dependencies: pkg/profiles requires pkg/cal
7276    o pkg/profiles:
7277     - added option ALLOW_PROFILES_GENERICGRID
7278         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
7279         that interpolation information (grid points and coefficients) is provided
7280         within the netcdf input files.
7281         -> sample matlab scripts can be found in MITgcm_contrib/gael
7282         that allow you to prepare netcdf input files.
7283     - also modified: cleaner include statements, cleaner error print statements,
7284       cleaner stops when error, and more tests of the netcdf input files consistency.
7285    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
7286    o pkg/seaice:
7287     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
7288       requires a new routine: seaice_diagnostics_fill.F
7289     - make sure that seaice does not move if not forced (pressure replacement
7290       method, Hibler and Ip, 1995), changes results
7291     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
7292     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
7293       It is turned off by default (=-1.), because it changes the results.
7294     - make it possible to read AREA from a file, too.
7295    
7296    checkpoint59c (2007/06/04)
7297    o add S/R and diagnostics for oceanic mixed-layer depth
7298    o move GMRedi call after all vertical mixing schemes (including KPP)
7299    o pkg/thsice:
7300     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
7301      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
7302    o pkg/obcs:
7303     - bug fix for balance code
7304    o pkg/seaice:
7305      - allow values of SEAICE_elasticParm > 1
7306      - add new parameter SEAICE_evpTauRelax as an alternative
7307        to SEAICE_elasticParm
7308      - make lsr boundary conditions free slip (by default), changes result
7309      - add code for no slip boundary conditions for lsr
7310      - set minimum of zeta to zero (and not 4e8) (changes results)
7311      - add a cap on AREA after advecting AREA if seaice_growth is not called
7312    o change calculation of Visbeck K:
7313      - no longer depend on tapering scheme; instead, compute slope (limited
7314        by GM_maxSlope). this is equivalent to what was comuted before with
7315        clipping or linear tappering.
7316      - fix vertical averaging (wrong by 1/2 level)
7317      - leave the old version (but will not be maintained) within
7318        #ifdef OLD_VISBECK_CALC / #endif
7319      - update output of exp. ideal_2D_oce
7320    o change error catch in calc_r_star to improve vectorization
7321    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
7322      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
7323    o adjoint:
7324      Re-organized adjoint checkpointing according to Matt Mazloff
7325      (but with modifs/completions/cleanups)
7326      Storing is now bundled into large arrays to optimized I/O
7327      (and second step in cleanup of the_main_loop)
7328    
7329    checkpoint59b (2007/05/16)
7330    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
7331      - export/import (between ocean & coupler) fields needed for ocean DIC.
7332    o pkg/seaice:
7333      - get rid of three more exchanges seaice_calc_viscosities (required
7334        different loop boundaries in seaice_lsr and seaice_ocean_stress)
7335      - bug fix in seaice_ocean_stress (update of lab_sea required)
7336      - reduce loop boundaries to necessary minimum also in seaice_evp
7337      - go back to the old way of computing deltaC/Z as the adjoint likes that
7338        better
7339    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
7340      passive tracer to an Age Tracer) + update output.txt
7341    o pkg/exf:
7342      - implement A-grid / C-grid selection for wind-stress input files.
7343      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
7344      for now, in exf_bulk_largeyeager04.F only :
7345      - change implementation for case where windspeed + 2. components wind-stress
7346        are read-in. AND use rhoConstFresh to convert evap.
7347    o pkg/seaice:
7348      - use correct EXCH_UV for wind-forcing (on A-grid).
7349      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
7350        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
7351    o pkg/exf:
7352      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
7353      EXF_INTERPOLATION:
7354      - merge global_with_exf/code version of exf_interp_read.F
7355        to the main code ;
7356      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
7357        reading the file ; Important: This options needs to be defined to recover
7358        previous code.
7359        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
7360      - no longer loose real*8 precision along the way when using exf_iprec=64.
7361    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
7362      - change discretisation of evp-solver in order to avoid another exchange
7363        (changes lab_sea) and clean up a little
7364      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
7365        help the adjoint (this also changes the results slightly)
7366      - add a few "_d 0" where they had been missing in seaice_evp.F
7367      - cleaning up: remove unused seaice_calc_rhs.F
7368    o pkg/exf: some cleaning-up:
7369      - change various "constants" into runtime parameters
7370      - cleaned-up Large&Yeager04 routine which should eventually
7371        replace exf_bulkformulae.F (changed names of S/R and CPP)
7372        and merged various ALLOW_ATM_WIND options
7373     only used with thsice pkg (in thsice_get_exf.F):
7374      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
7375        which are used when useStabilityFct_overIce=TRUE (= the default)
7376      - change default values of ice & snow emissivity and scale downward LW
7377        by ice & snow emissivity.
7378    o pkg/thsice:
7379     fix few little problems, in thsice_calc_thickn.F:
7380      - growth vertically (and not laterally) if iceFrac == iceMaskMax
7381      - melt only laterally if hIce < hThinIce (as the comments say)
7382      and in thsice_extend.F:
7383      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
7384      - start to form ice as soon as the minimum ice-volume is reachable.
7385     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
7386      and cpl_aim+ocn
7387    o pkg/kpp
7388     - move computation of surface related input fields to KPP into a new
7389       subroutine kpp_forcing_surf.F
7390     - remove wrong (within bi,bj loops) EXCH calls.
7391     - little cleaning (add argument myThid in last position, cvs header ...)
7392     - for now, fix conservation problem by exchanging KPPviscAz (may not
7393       be the best fix)
7394    o pkg/seaice
7395     - check for inconsistent evp parameter/cpp-flag combination
7396     - remove leftover errIO flat for obsolete name list error handling
7397    o OpenAD
7398     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
7399    
7400    checkpoint59a (2007/05/01)
7401    o pkg/seaice: some parameter clarifications and a little bit of clean up
7402    o pkg/thsice: rename run-time parameters:
7403       himin       -> hIceMin
7404       himin0      -> hThinIce
7405       hihig       -> hThickIce
7406       i0          -> i0swFrac
7407       transCoef   -> bMeltCoef
7408       frac_energy -> fracMelting
7409      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
7410       with default values (for now) that do not change the results.
7411      remove old version of thsice vars advection in pkg/seaice.
7412    o in FFIELDS.h:
7413      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
7414      - make pLoad & sIceLoad always available (but still only used if
7415         ATMOSPHERIC_LOADING is #define).
7416    o pkg/kpp: replaced _KPP_RL with _RL
7417    o bug fixes for vertical diffusivity computations when both KPP and
7418        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
7419        are no longer updating the vertical diffusivity array
7420        (passed as argument) but are (re-) setting those arrays.
7421    o pkg/seaice: fix bug in evp solver, while doing that
7422      - change (improve?) discretization of stress computations for both
7423        cgrid-lsr and evp solver
7424      - add a new routine to compute strain rates
7425      - the above changes lab_sea results
7426      - add no slip conditions for evp solver (off by default), lsr-version
7427        may follow
7428      - fix exchange for shear at Z-points (does not change lab_sea)
7429      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
7430        (to force the user to pick a time step since there is not "safe" way
7431        of choosing it)
7432      - add principal stress diagnostics
7433      - rearrange fields for evp a little to avoid having to call a: too many
7434        exchanges and b: exchanges for stress trensor components which we do
7435        not have.
7436      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
7437        of evp, complete rewrite for lsr case (latter is does not yet work
7438        in all cases)
7439    o pkg/kpp: add code to have mixing in shelf ice caverns
7440      - add myThid to all kpp routines (long overdue)
7441    
7442    checkpoint59 (2007/04/19)
7443    o pkg/exf:
7444      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
7445        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
7446      - move exf header files from lower_case.h to UPPER_CASE.h ;
7447        add missing cvs Header & Name
7448      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
7449      - add namelist param. selectStressGridPosition, exf_monFreq
7450      - retire many _CLIM routines, and remove data.exf_clim
7451        + params moved to data.exf
7452        + climsst, climsss now handled by exf_set_gen, i.e.
7453          climss?period=0 refers to constant field,
7454          climss?period=-12 to monthly forcing
7455      - split up namelists in data.exf
7456    o pkg/seaice:
7457      - remove seaice_exch and seaice_exch_uv
7458      - remove superfluous exchange of theta
7459      - add myThid to seaice_budget_ocean/ice
7460      - add new interface for atmospheric wind forcing (C-grid only)
7461        + new routine
7462        + two new field (taux, tauy for stress over ice)
7463        + removed one global field (DAIRN) for C-grid case only
7464    o pkg/thsise
7465      - 2nd set of modifs for thsice adjoint in conjunction with exf
7466    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
7467    
7468    checkpoint58y_post (2007/04/15)
7469    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
7470      vertical diffusivity, similar to that in MOM4; turned on using
7471      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
7472      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
7473    o Added capability for 3D specification of background vertical diffusion
7474      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
7475      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
7476      "data" file that contains the 3D vertical diffusivity coefficients.
7477    o ice dynamics (pkg/seaice) with thsice thermodynamics:
7478      - add code within pkg thsice to advect & diffuse sea-ice fields
7479      similar to (and will replace) what has been added in  seaice_advdiff.F,
7480      but: - conserving Mass, Heat & Salt.
7481           - better when using non-linear advection scheme (not yet fully tested)
7482           - can also be used in atmospheric set-up (for now, only the diffusion).
7483    
7484    checkpoint58x_post (2007/04/04)
7485    o IO option for global-file compact format:
7486      - add options when generating topology (utils/exch2/matlab-topology-generator)
7487      - add I/O capability (pkg/mdsio).
7488      - adapt utils/matlab/rdmds.m to read this format.
7489      for now long-line format not yet supported by pkg/mdsio (& exch2).
7490    o shelfice: add a few diagnostics
7491    
7492    checkpoint58w_post (2007/03/13)
7493    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
7494      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
7495      (and replace horiVertRatio in NH code).
7496      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
7497                         and tutorial_plume_on_slope (sensitive to truncation)
7498    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
7499      directly to drive seaice model (C-grid only)
7500    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
7501     - reintroduce computation of wind from stress,
7502     - compute tau (in exf_bulkformulae.F) from windstress averaged to
7503       mass points to avoid tau = 0
7504     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
7505    o rdmnc.m: make it work with "global" files created with gluemnc
7506    o rdmnc.m : some improvements in dealing with singleton dimension
7507      (tested on all testreport mnc output files).
7508    o genmake2: disable pkg/profiles if netcdf test fails.
7509    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
7510    o move call to cal_readparms up to make calendar parameters/variable available
7511      to all packages
7512    
7513    checkpoint58v_post (2007/02/08)
7514    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
7515      useDynP_inEos_Zc tested.
7516    o pkg/exf: changes to properly interpolate/mask/scale initial fields
7517    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
7518      and portions thereof.  See read_cs.txt for description and examples.
7519    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
7520      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
7521      following the great-circle arc between those 2 points.
7522    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
7523      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
7524    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
7525     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
7526     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
7527     - still needs work (not working with some options ; efficiency to improve)
7528       and serious testing.
7529     - use this scheme for temperature & salinity in 2 advection test exp.:
7530       advect_xy & advect_xz, respectively.
7531    
7532    checkpoint58u_post (2007/01/12)
7533    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
7534    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
7535    o testreport: add option "-skipdir" to skip some test.
7536    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
7537      momentum calculation.
7538    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
7539    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
7540      remove checkpoint.F and the_correction_step.F (no longer used);
7541      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
7542    o add option (linFSConserveTr) to correct for tracer source/sink due to
7543      Linear Free surface
7544    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
7545    o pkg/thsice: fix reading mnc-pickups
7546    
7547    checkpoint58t_post (2006/12/30)
7548    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
7549    o pkg/mdsio:
7550     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
7551       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
7552       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
7553     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
7554     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
7555       either MDS_READ_FIELD or MDS_WRITE_FIELD )
7556     - new S/R (to replace MDSWRITEMETA), which allows to write more
7557       informations (variable names, time ...) to meta files.
7558     - modify rdmds.m to give back the meta file content.
7559    o pkg/diagnostics: change vertical interpolation to be safer, and more
7560       flexible (define p-levels to interpolate to in data.diagnostics);
7561      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
7562       diagnostic pointer.
7563    o pkg/seaice: more cleaning up of seaice_growth, added many comments
7564    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
7565    o fix multi-category seaice:
7566     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
7567       SEAICE_MULTICATEGORY
7568     - fix short wave heat flux
7569    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
7570       and allow to use EVP solver. Change forward lab_sea: test both EVP
7571       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
7572    o Initial check-in of lab_sea adjoint
7573      (very similar to natl_box_adjoint/code_seaice)
7574      * used C-grid and EVP solver
7575      * used KPP, GM/Redi
7576      * uses inAdExact=.TRUE.
7577      * gradient checks fail for both ADM and TLM
7578        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
7579        f.d. gradients actually seem more problematic than ADM, TLM gradients;
7580        issue is related to forward mismatch between g77 an ifort
7581    o pkg/seaice: overhaul of thermodynamics
7582     - growth.F and groatb.F are replaced by new routine seaice_growth.F
7583     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
7584     - move a few global fields out of SEAICE.h into seaice_growth.F and
7585       make them 2D (FICE/QNETO/ ...)
7586     - remove FO (it is the same as QNETO)
7587     - introduce a few local fields to avoid modifying external fields such
7588       as atemp, etc.
7589    
7590    checkpoint58s_post (2006/12/11)
7591    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
7592      changed exf_set_gen.F so that
7593        genperiod=0 means input file is one time-constant field and
7594        genperiod=-12 means input file contains 12 monthly means
7595    o CG2D: use pre-computed solver main-diagonal (stored in common block);
7596      this affects truncation error ; generate new output file for exp. which
7597      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
7598        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
7599        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
7600        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
7601        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
7602        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
7603    o start implementation of deep-atmosphere and anelastic formulation
7604    o verification: remove 2nd copy of input files and use script "prepare_run"
7605      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
7606    o mom_common/vecinv/fluxform: fix a few initialisation isssues
7607    o profiles: fix for multithreaded case
7608    
7609    o diagnostics: rename few diags:
7610      s/'PRESSURE'/'RCENTER '/g
7611      s/'TICE    '/'oceFreez'/g
7612      s/'TAUX    '/'oceTAUX '/g
7613      s/'TAUY    '/'oceTAUY '/g
7614      s/'SWFLUX  '/'oceQsw  '/g
7615      s/DIFx/DFxE/g
7616      s/DIFy/DFyE/g
7617      and add few ocean-forcing diagnostics:
7618      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
7619    o modifications to pkg/seaice/growth.F and budget.F, which change results of
7620      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
7621      as actual snow thickness.  It now refers everywhere to effective snow
7622      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
7623    
7624    checkpoint58r_post (2006/11/17)
7625    o modifications to pkg/seaice/growth.F, which change results of
7626      lab_sea experiment: fixes pertain to melting snow over open water, to
7627      masking EVAP under sea ice, and to using the correct AREA variable for
7628      computations of EVAP, PRECIP, HSNOW, and GHEFF
7629    o add ability to read bathy, salt, and theta using MNC (off by def)
7630    o add flooding algorithm and advection of HSNOW for pkg/seaice;
7631      both are turned off by default and do no change any results
7632    o seaice advection with pkg/thsice: a step toward the use of non-linear
7633      advection scheme, but #ifdef or commented out for now (requires more EXCH).
7634    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
7635      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
7636      in natl_box (affects results @ truncation level: update output.txt)
7637    o multi-threading and IO:
7638      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
7639      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
7640        (needed to work with SingleCpuIO): tested in all verif. exp.
7641    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
7642      affects the results (but none of the verification test uses this scheme).
7643    o Adding some pkg/diagnostics capability to pkg/seaice
7644      (will certainly be subject to changes)
7645    o ctrl: adding new control variables:
7646      lwflux, lwdown, evap, snowprecip, apressure, runoff
7647    
7648    checkpoint58q_post (2006/10/20)
7649    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
7650      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
7651      high_res_cube configuration by 4% on Columbia.
7652    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
7653      add (in global_with_exf/code) a version of EXF_INTERP_READ without
7654      dynamical allocation (seems to work in multi-threaded).
7655    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
7656      single CPU io) so that TAF does not have to see EESUPPORT.h
7657    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
7658    
7659    checkpoint58p_post (2006/09/08)
7660    o obcs: stop if obcs is used with useCDscheme = .true.
7661    o shelfice:
7662     - fix a sign error so that no slip at shelfice interface works
7663     - remove stop for combination non-hydrostatic code and shelfice. That does
7664       not mean, that the results are correct, but at least they are numerically
7665       stable
7666    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
7667    o added adjoint exch routined for all exch*3d* routines
7668      and updated flow directives
7669    
7670    checkpoint58o_post (2006/08/28)
7671    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
7672      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
7673    o change controling S/R for writing pickup file (new S/R do_write_pickup)
7674      and clean-up reading/writing of pickup files.
7675    o fix local version of read/write pickup (NH part) in rotating_tank/code
7676    o simplify EXCH interface:
7677     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
7678     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
7679    o added the regrid package
7680    o shelfice:
7681     - add a simple boundary layer scheme to reduce noise
7682     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
7683    
7684    checkpoint58n_post (2006/08/14)
7685    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
7686       local variable (not in common block).
7687    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
7688      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
7689      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
7690        to work with SingleCpuIO.
7691    o add "_d 0" to real constant of pkg/cfc subroutines ;
7692       update exp. cfc_exemple & tutorial_cfc_offline output files.
7693    o multi-threading and IO:
7694      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
7695        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
7696      - barrier before and after reading.
7697      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
7698      - avoid using MDS_WRITELOCAL for LAND pkg output.
7699      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
7700        common-block variables ; Allows multi-threading with master-thread IO.
7701    o change default MAX_NO_THREADS from 32 to 4 ;
7702      and stop cleanly when MAX_NO_THREADS is too small.
7703    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
7704    
7705    checkpoint58m_post (2006/07/17)
7706    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
7707       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
7708    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
7709       keep global_ocean.90x40x15 (for AD testing) with former secondary test
7710       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
7711    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
7712        add MITgcm_tutorials (= code + all the tutorials)
7713    o ecco, option to compute cost for total ssh (mean+anom)
7714    o consistent with addition of ptracer and ssh in pkg/profiles
7715    o profiles: adding ptracer and ssh
7716    o testreport: change multi-test output-file name
7717      (from output.txt.{name} to output.{name}.txt)
7718    o profiles: now ok for mutli-tiles case
7719    o seaice: add 4 parameters for different advection schemes for area,
7720      (effective) seaice thickness, enthalphy, and snow height. Their default
7721      is the standard parameter SEAICEadvScheme
7722    o calc_gw:
7723     - add cosFacU in zonal viscous flux (harmonic.visc.).
7724     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
7725       of tutorial_plume_on_slope.
7726    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
7727    o calc_gw: true flux-form, account for horizontal grid spacing.
7728      update rotating_tank results, but not plume_on_slope (affected at
7729      truncation level, 11 digits).
7730    
7731    checkpoint58l_post (2006/07/12)
7732    o calc_gw:
7733     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
7734     - remove side-drag for now (need to fix it); update plume_on_slope results.
7735     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
7736    o commit code to make SST/SSS weights spatially variable
7737      (based on either variable in-situ or variable initial T/S weights)
7738    o pkg/ecco:
7739      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
7740        now based on horizontally varying weights wthetaLev, wsaltLev
7741      * cost_averagesflags now returns year indices in addition to day, month
7742      * sflux balance is performed on annual basis
7743        (sflxumm, sfluxmm2, bal_sfluxmm)
7744      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
7745        including separate counting and multipliers
7746    o pkg/rbcs
7747      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
7748    
7749    checkpoint58k_post (2006/07/06)
7750    o testreport:
7751     - always build in dir. "build" (if not there, mkdir build instead of building
7752       & running in input)
7753     - run in dir run (if it exists), in build otherwise.
7754     - call prepare_run (if input/prepare_run exists)
7755     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
7756    o pkg/exf modifications to interpolation and rotation routines for more
7757       reasonable treatment of North Pole singularity: for tracers North Pole
7758       value is set to northernmost zonal-mean value, for zonal velocity it is
7759       set to zero, and for meridional velocity it is set to northernmost value.
7760    o pkg/exf/exf_check_range.F
7761     - add tile index to diagnostics and move stop statement to the very
7762       end of the routine.
7763    o pkg/diagnostics: (diagnostics_main_init.F)
7764      define title of isomorphic variables according to the current config.
7765    o pkg/thsice with pkg/seaice dynamics:
7766    - fix domain of computation (interior only, required for exf) and do exchanges
7767    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
7768    o towards a standard way of dealing with multi-threading in MONITOR
7769      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
7770    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
7771       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
7772    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
7773    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
7774    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
7775       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
7776    o tracer advection:
7777     - clean-up and simplify calc_common_factors.F
7778     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
7779       advection subroutine (but still not used within DST advection S/R)
7780    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
7781    
7782    checkpoint58j_post (2006/06/15)
7783    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
7784      from file (collects calls previously in FORWARD_STEP)
7785    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
7786    o adjoint store dir. adjusted accordingly
7787    o genmake2
7788      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
7789    
7790    checkpoint58i_post (2006/06/14)
7791    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
7792      on wind stress (SEAICEstressFactor defaults to 1.)
7793    o Total number of Timers is finite (<=40): comment out 2 non-essential one
7794      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
7795    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
7796      on CS-grid: no longer loosing mass.
7797    o exf & curvilinear-grid: no longer modify longitude xC & xG.
7798    o pkg/ggl90: fix sloppy output and fix a bug
7799    o pkg/seaice: added SEAICEuseEVPpickup parameter
7800      - Set to false in order to start EVP solver with
7801        non-EVP pickup files when using SEAICEuseEVP
7802      - fix sign error in diffusion in seaice_calc_rhs
7803    
7804    checkpoint58h_post (2006/06/07)
7805    * Modifications for bottom topography control
7806      o replace hFacC by _hFacC at various places
7807      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
7808      o add non-self-adjoint cg2d_nsa
7809      o update autodiff support routines
7810      o re-initialise hfac after ctrl_depth_ini
7811      o works for 5x5 box, doesnt work for global_ocean.90x40x15
7812    * Adding verification for 5x5 box (4-layer) bottom topography control
7813    
7814    checkpoint58g_post (2006/06/07)
7815    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
7816       used for mean seasonal cycle, mean diurnal cycle); add an example
7817       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
7818    o pkg/ggl90:
7819      - add parameter (minimum surface kinetic energy)
7820      - fix bug (avoiding division by zero)
7821    o couple pkg/thsice to pkg/seaice:
7822      - modify advection in seaice to accomodate new scalar fields to be advected
7823      - only muliDimAdection scheme work with seaice/thsice
7824      - mapping of thsice-variables to seaice-variables, back and forth
7825      - does not break the verification experiments, but does not give the
7826        desired results either
7827    o pkg/seaice
7828      - make (default) second order advection a bit less confusing?
7829    
7830    checkpoint58f_post (2006/06/05)
7831    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
7832      to pkg/seaice):
7833      - new routines thsice_map_exf and thsice_get_exf provide the interface
7834      - add an additional formal parameter to thsice_solve4temp
7835    o pkg/exf:
7836      - add new fields wspeed, snowprecip (to be able to couple to thsice)
7837      - correct Stefan-Boltzmann constant
7838      - new parameter for longwave surface emittance
7839      - separate some stuff from exf_bulkformulae into new routines  
7840        exf_radiation, exf_wind
7841      - add new parameters and constants: longwave emissivity for ocean, ice
7842        and snow, evaporation parameters over ice
7843      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
7844        either wind from stress or stress from wind
7845    o pkg/thSIce:
7846    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
7847    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
7848       and THSICE_CALC_THICKN
7849    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
7850    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
7851      to make debugging easier.
7852    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
7853    o pkg/bulk_force:
7854      - clean-up comments and parameters ;
7855      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
7856    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
7857      generate new output for test-experiment: aim.5l_cs.thSI
7858    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
7859      testreport accordingly
7860    
7861    checkpoint58e_post (2006/05/17)
7862    o SEAICE_CGRID adjoint done
7863    o R_STAR adjoint implemented.
7864      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
7865      * need to sort out init. of h0facc, etc.
7866    o Make pkg/profile fully independent of ecco,cost, etc. stuff
7867      to be able to use it in pure forward.
7868    
7869    checkpoint58d_post (2006/04/21)
7870    o upgrade simple test-experiment to tutorial example:
7871     step.1: duplicate the experiment and (step.2) will remove the old copy.
7872      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
7873      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
7874      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
7875      tutorial_global_oce_biogeo    <- copy of dic_example
7876      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
7877      tutorial_plume_on_slope       <- copy of plume_on_slope
7878      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
7879      tutorial_global_oce_optim     <- empty for now (David ?)
7880      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
7881     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
7882    o correct a sign problem in cost_scat.F
7883    o obcs and ptracers: fix boundary conditions for advections schemes
7884      with larger stencil
7885    o thsice adjoint: start
7886    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
7887      completeness
7888    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
7889      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
7890    o ptracers adjoint:
7891      * avoid extensive recomputatations
7892      * fix missing re-init. of gptr (missed by TAF)
7893    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
7894      me to turn off the excessive output to STDOUT that this package produces
7895    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
7896      and add those terms in Vector-Invariant formulation.
7897    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
7898      if the control period (xx_hfluxperiod etc) is 0
7899    o in profiles pkg, clean routines and fix details
7900    o in ecco pkg, reading ssh data:
7901      fix problem in case the model does not start at iter0=0
7902    o fix mnc-pickup/restart for ptracers
7903    o new package prifiles:
7904      code to compute profile-based cost by Gael Forget
7905      (modifs in ecco, ctrl, autodiff)
7906    o Benign bug fix in initialization (spotted by M. Mazloff) of
7907      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
7908    
7909    checkpoint58c_post (2006/03/23)
7910    o adjoint: finish NLFS adjoint and provide reference output in
7911      verification/global_ocean.90x40x15/results_ad_nlfs
7912    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
7913      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
7914      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
7915      with SEAICE_CGRID defined.
7916    o move calendarDumps from "data" to "data.cal" and clean-up the code
7917      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
7918    o add useEXF & useCAL flags (for now, set in hard-coded way)
7919    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
7920      (were missing in NH mode, and wrong in quasihydrostatic mode).
7921      waiting for Chris updated version of calc_gw to add those CALLs.
7922    o fix bug in quasihydrostatic S/R ;
7923      add a test for this option: global_ocean.90x40x15.qshyd
7924    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
7925      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
7926    o add on/off flag useOffLine for package OFFLINE
7927    o seaice:
7928      - modify advection so that it works also on the C-grid
7929      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
7930        problem in multi-tile runs with C-grid
7931      - add flags for clipping ice velocities and/or masking solver forcing
7932      - fix drag (ocean on ice) formulation and a bug that caused noise in the
7933        C-grid solver
7934      - added a few comments to seaice_diffusion.F
7935      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
7936        are now exclusive)
7937      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
7938        required re-ordering the code a little:
7939       + make DAIRN global variable (defined in SEAICE)
7940       + move computation of the viscosities eta and zeta into a new separate
7941         routine (because I need to recompute them in seaice_ocean_stress.F)
7942    
7943    checkpoint58b_post (2006/03/13)
7944    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
7945      update output.txt of exp. aim.5l_cs.thSI
7946    o various mnc cleanups and improvements:
7947      + shrink lookup tables by factor of ~4
7948      + better error reporting when running out of lookup space
7949      + able to handle longer path/file names (up to 500 chars)
7950    o adjoint:
7951      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
7952      - TBD: "hidden" mom_vecinv recomp. in dynamics
7953    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
7954     (allow to differentiate between forcing components using new integer flags:
7955      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
7956     and add new flag to put Dissipation tendency out of Adams-Bashforth.
7957    o ecco
7958      - enable trend removal from SSH anomaly obs.
7959    o adjoint
7960      - a fix for PmEpR when #undef EXACT_CONSERV
7961      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
7962      - try to fix "hidden" recomp. in forward_step for NLFS
7963        (NLFS seems broken sometimes after I checked it in)
7964    o seaice:
7965     - add c-grid version of the dynamic solver:
7966       + three new routines that are the c-grid substitute lsr, dynsolver
7967         and ostres
7968       + put a few fields that were local to dynsolver into global common
7969         blocks, so that I can move the computation of stresses etc into
7970         seaice_lsr (saves coding but may break the adjoint).
7971     - replace more hardwired parameters by runtime parameters
7972     - add ice masks that mask the rhs of the implicit solvers where there
7973       is no ice (commented out in seaice_dynsolver, because i am not sure
7974       if this works properly), eventually this should replace the clipping
7975       of ice velocities in seaice_dynsolver to +/-40cm/s.
7976    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
7977      include it only where its needed
7978    o move balancing of fluxes before the call of external_forcing_surf
7979    o seaice:
7980      - correct units of turning angles (now they are really in degrees)
7981      - move computation of GWATX/Y out of main routine into dynsolver
7982      - initialize GWATX/Y in seaice_init
7983    o Apply mask on Fresh-Water flux (needed for SSH forcing).
7984      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
7985    o seaice: add runtime flags for turning angles (default to zero)
7986    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
7987      and trend from exf forcing and ctrl control adjustments
7988    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
7989      (since checkpoint57x_post)
7990    o change the default rotation period to 86164.s = the Earth rotation
7991    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
7992      and based on a reference stratification. Tested within hs94.cs-32x32x5.
7993    o seaice advection: add code for choosing between the default (2nd order
7994      central differences) and multiDim advection schemes provided by
7995      pkg/generic_advdiff
7996    o seaice:
7997      - removed all references to SEAICE_GRID.h fields from
7998        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
7999        (cubed-sphere configuration will change a little)
8000      - grid computations in seaice_init are obsolete now.
8001      - cleaned up code a little so that is easier to read (hopefully).
8002      - added new (better?) discretizations of default advection and diffusion
8003        (turn on with SEAICEuseFluxForm)
8004      - replace 1 in 3d global fields by kSurface in growth.F
8005      
8006    checkpoint58a_post (2006/02/13)
8007    o seaice:
8008      - bug fix in advect.F
8009    o shelfice:
8010      - separate shelfice load anomaly from pload (breaks with time
8011        dependent forcing), => introduce constant field shelficeLoadAnomaly.
8012        Its default is 0., but it may be computed more cleverly from (unknown)
8013        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
8014        done offline. A good approximation of the pressure load anomaly is
8015        necessary to avoid large initial adjustment processes underneath
8016        deep-reaching shelfice.
8017      - small fix in ISOMIP shelfice_thermodynamics
8018      - add more sophisticated thermodynamics of Hellmer (1989), this is
8019        now the default
8020      - give a few constants more intuitive names
8021    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
8022      if bulk formulae are used in long integration (especially EmPmR). Turn
8023      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
8024      if balancePrintMean, the imbalance that is substracted is printed to
8025      STDOUT.
8026    o fix bug (typo) in obcs_apply_eta.F
8027    o add a new package shelfice which enables us to model the circulation
8028      underneath shelf-ice with draughts of hundreds of meters.
8029     - works
8030     - to do: + include improved thermodynamics
8031              + check whether kSurfC (from model/inc/SURFACE.h) can be used
8032                instead of new field kTopC
8033              + can we use topoFile, Ro_surf and existing code in ini_depth.F
8034                instead of new field R_shelfIce and new code in ini_depth.F
8035                and ini_mask_etc.F?
8036              + adjust vertical mixing schemes?
8037    o seaice pkg:
8038     - add a cpp-flag to include a simple formula for a salinity dependent
8039       freezing point of sea water at the surface
8040     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
8041       meridional stresses are now different (and hopefully correct)
8042    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
8043       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
8044       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
8045    o pkg/diagnostics: add options and parameters for regional-statistics
8046       diagnostics ; define regions by reading a region-mask from a file
8047       (might add other options later)
8048    o pkg/bulk_force:
8049     - add option and parameters to use AIM surface-flux formulae.
8050     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
8051       others forcing fields (defined in PARM05, parameter file "data") are loaded
8052       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
8053     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
8054     - use the right EXCH call for uwind,vwind (to work on CS-grid).
8055     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
8056       and parameters (note: calcWindStress replaces .NOT.readwindstress).
8057     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
8058    
8059    checkpoint58 (2006/01/12)
8060    o add "--embed-source" option to genmake2 which, when the supporting
8061      tools can be compiled (as determined by genmake2) will turn on the
8062      embed_files package which then embeds the entire MITgcm source code
8063      (*.[fFhc] + Makefile) used for the build within the executable
8064      - requested by CNH but off by default
8065      - adds a paltry <9MB to the mitgcmuv executable in most cases
8066      - only writes the output when useEMBEDSRC in eedata is true
8067    o clean up 3-dim. relaxation codes:
8068      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
8069      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
8070      * Thanks to Tom Haine for testing!
8071    
8072    checkpoint57z_post (2005/12/31)
8073    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
8074      affects output (@ truncation level) of exp. plume_on_slope ; updated.
8075    o fix the pickup behavior for obcs in combination with ptracers
8076    o fix a bug in ptracers_external_fields_load
8077    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
8078      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
8079    o transfered surface NH pressure to eta field (if exactConserv).
8080    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
8081         and update lab_sea output.txt file.
8082    o completing 3-dim. relaxation code: additional term
8083         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
8084      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
8085      * At compile time, in "EXF_OPTIONS.h" set
8086          #define  ALLOW_CLIMTEMP_RELAXATION
8087          #define  ALLOW_CLIMSALT_RELAXATION
8088      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
8089          tauThetaClimRelax3Dim = 15552000.0,
8090          tauSaltClimRelax3Dim  = 15552000.0,
8091      * 3 cases:
8092          1) Use a constant-in-time 3-dim. field
8093          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
8094          3) Real-time relax. to time-evolving prescribed field
8095    o Adding Laplacian-type smoothness constraint on
8096      initial and boundary (forcing) controls (ic, bc)
8097      * enable at compile-time via
8098        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
8099      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
8100      * Absolute scale somewhat unclear so far
8101      * no area weighting was included since no other cost term does so far
8102    
8103    checkpoint57y_post (2005/12/08)
8104    First step for a NLFS adjoint
8105    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
8106    o new init. routines for calc_r_star, calc_surf_dr
8107    o still need to deal with ini_masks_etc
8108    o testreport seemed happy
8109    checkpoint57y_pre (2005/12/08)
8110    
8111    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
8112    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
8113    o add new offset feature to offline pkg (plus minor cleanup)
8114    o cfc fixes for final year of integration
8115    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
8116      be in GCHEM_OPTIONS).
8117    
8118    checkpoint57x_post (2005/12/04)
8119    o fix testreport Pb in multiple test experiment.
8120    o cleanup our namelist syntax in verification:
8121      - make it more F95 standards compliant (some work still needed)
8122      - allows the vast majority of our tests to work with gfortran
8123    o Non-Hydrostatic:
8124     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
8125     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
8126    o Allow to apply AB on T,S rather than on AB(gT,gS):
8127     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
8128     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
8129       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
8130     - need a "clever" read_pickup to restart from the other AB formulation
8131    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
8132    o remove some unused variables (reduces number of compiler warnings)
8133    o adjoint
8134      * Disable useVariableViscosity for adjoint for time being
8135        (there are a number of extensive recomputations)
8136      * Initialize certain variables needed for adjoint
8137    
8138    checkpoint57w_post (2005/11/03)
8139    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
8140                 fix the singleCpuIO RS version of MDSWRITEFIELD
8141       and add a WARNING if using globalFiles=T with multi-processors.
8142    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
8143      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
8144    o tracer advection scheme:
8145      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
8146       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
8147       was not very convenient).
8148      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
8149       (further tests needed for the implicit DST & Flux-Limiter schemes).
8150    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
8151      and sRef for convenience, handy, when you want to initialize
8152      ptracers in a large domain with a constant non-zero value. Also,
8153      untangle ptracers_init.F a little.
8154    
8155    checkpoint57v_post (2005/10/13)
8156    o change dome exp. to use variable viscosity in side-drag terms.
8157    o remove all the files from the cfc_offline test since they are now
8158      incorporated into tutorial_cfc_offline which has been producing
8159      identical results for a few days of testing
8160    o add new parameter: sideDragFactor to enable half-slip-side BC
8161      and change side-drag S/R to use viscosity from mom_calc_visc
8162      (can switch back by setting sideDragFactor=0.); affects results at
8163      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
8164       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
8165    o vorticity & strain are now computed without masking, to account for
8166      no-slip-side BC in variable viscosity calculation ; mask is applied
8167      anyway later on, before computing advection/coriolis terms.
8168    o modify exp4 to test new obcs support for reading from external files
8169      and for passive tracers
8170    o fix behavior of ptracers_monitor when monitor output is written to a
8171      netcdf-file; still not independent of monitor.F (writes in the same
8172      file).
8173    o change default value of tRef (put a uniform, meaningful value for ocean
8174      & atmos) and initialize sRef (was missing, as Martin mentioned).
8175    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
8176      to be proportional to enstrophy dissipation length.  Thus,
8177       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
8178      This is now consistent with Smagorinsky and with the manual.
8179    
8180    checkpoint57u_post
8181    o OBCS and PTRACERS: add open boundary support for passive tracers
8182      - either use homogenous (pseudo) v.Neumann conditions or prescribe
8183        OB-values from file; this is not different from the way theta and salinity
8184        are treated
8185      - however, Orlanski-radiation conditions are not supported, and the model
8186        will stop if you use pTracers and Orlanski at the same time.
8187      - beefed up the rountine obcs_external_fields_load: now only those open
8188        boundary values are overwritten with values from files for which there
8189        are really files, otherwise the OB-fields remain untouched. This makes
8190        it possible to use different OBs at different ends of the domain (as
8191        with EXF)
8192    o reduce number of exch calls in shap_filt (s2).
8193    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
8194      truncation level) 4/5 MLAdjust test results (11&12 digits match).
8195    
8196    checkpoint57t_post (2005/10/03)
8197    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
8198    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
8199      same truncation, independent of the face number: affects affects several
8200      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
8201    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
8202      note that biharmonic viscosity + no-slip was not tested in any experiment.
8203    o fix bug in non-linear free-surf side-drag ; generate new output for
8204      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
8205    o make mnc honor the writeBinaryPrec flag for most kinds of output
8206    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
8207    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
8208      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
8209    o add brackets in multi-terms sum to get same truncation, independent of
8210      the face number (manage to get exactly same value of gU,gV at the cs-edge)
8211      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
8212    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
8213      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
8214      a maximum grid-scale Reynolds number.  Also, changes all length calculations
8215      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
8216      Suggested values of viscosity parameters found in mom_calc_visc.
8217      Many new viscosity diagnostics available.
8218    
8219    checkpoint57s_post (2005/09/20)
8220    o Add clearing-house for viscosity calculations, mom_calc_visc and
8221      correct numerous bugs in LeithD and Smagorinsky discretizations.  
8222      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
8223      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
8224      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
8225      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
8226      The Strain-Tension form is now called with useStrainTensonVisc=.true.
8227      ViscAhStrain and viscAhTension are now retired.
8228    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
8229    o In response to JMC's bug report, genmake2 now ignores any soft-links
8230      that it finds in the *current* directory when searching for files.
8231      Soft-links found in any other source directories will still work as
8232      they did before.
8233    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
8234      a C routine to unlimit the stack size
8235    o mnc-ify pkg/aim snapshot vars
8236    o mnc-ify pkg/land as requested by Daniel
8237    o various changes to mnc including:
8238      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
8239      - output can now be grouped so that all files within a group
8240          change the ITER portion of their names in lock-step together
8241      - can now read ("global") PER-FACE (in addition to PER-TILE) files
8242          and works with both EXCH1 and EXCH2 (but needs more testing)
8243      - writing works for all verification test cases w/ g77 on Linux
8244    
8245    checkpoint57r_post (2005/09/07)
8246    o make MNC variable initialization happen earlier
8247    o add diagnostics for (almost) each term of the momentum Eq.
8248    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
8249    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
8250    o remove MINIMAL_TAVE_OUTPUT option ;
8251      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
8252    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
8253      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
8254    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
8255    o add time-dependent SST, SSS control
8256    o cost terms in ecco/ modularized (new cost_generic.F)
8257    o cost_averages routines are modularized (new cost_averagesgeneric.F)
8258    o new infrastructure for seaice model vs. obs misfits in seaice/
8259      * driver from the_main_loop.F is seaice_cost_driver.F
8260      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
8261      * gradient check in Exp. 6a of natl_box_adjoint/
8262    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
8263      (see README file)
8264    
8265    checkpoint57q_post (2005/08/19)
8266    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
8267    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
8268      - bug was reported by Jean-Michel and Ian Fenty
8269    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
8270      update exp. cpl_aim+ocn output.
8271    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
8272      Needed for high-res. runs with large global files
8273      to be able to limit tapelev size
8274    o Changed some tests for adjoint:
8275      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
8276      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
8277      * global_ocean.90x40x15/ back to default 3-level checkpointing
8278    o Modifications to enable scripted COMMON to MODULE conversion
8279      * verification/OpenAD/code/ has necessary scripts and description;
8280      * converts, compiles and runs successfully;
8281    
8282    checkpoint57p_post (2005/08/01)
8283    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
8284    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
8285      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
8286    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
8287    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
8288      (was already the case for dissipation with mom_vecinv,
8289       and also the case for grad.PhiHyd when staggered-timeStep)
8290      This will allow to put dissipation out-off the AB time-stepping.
8291     Unfortunately, affects truncation error. Update output of exp. that "fails"
8292      (cg2d matching number) and leave the others for later: front_relax(10),
8293      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
8294      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
8295    
8296    checkpoint57o_post (2005/07/30)
8297    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
8298      (2) its ready to be documented during the 20050801 DocFest
8299    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
8300      for ideal_2D_oce and lab_sea on linux_ia32_g77
8301    o set to #undef CTRL_SET_OLD_MAXCVARS_30
8302      in global1x1_tot/code_seaice_adj to access indices 32, 33
8303      (worth another tag)
8304    
8305    checkpoint57n_post (2005/07/29)
8306    o adding precip control xx_precip 32
8307    o adding swflux control xx_swflux 33
8308    o Replacing 10 forcing penalty cost routines by 1 generic.
8309    o Implementing partitioning in time-mean and variable adjustment
8310      for atmos. state.
8311    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
8312    o in natl_box_adjoint:
8313      * updated exp 1 to 10
8314        (but does not have time-mean vs. variable split results yet)
8315    o updated global1x1/*_seaice_adj/
8316      to incorporate latest changes
8317    o enable useSingleCpuIO for mdsio vector routines
8318      (applies in particular to tapelev I/O)
8319    o removed inefficient K-loop in all active_file*control*.F
8320    
8321    checkpoint57m_post (2005/07/28)
8322    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
8323      and advect_cs (use EXCH-2 and standard cs-32 grid files).
8324    o pkg/exch2: filling of face-corner halo regions is optional
8325      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
8326    
8327    checkpoint57l_post (2005/07/14)
8328     tag before updating tutorials (pre-release-2)
8329    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
8330       for output and interpolation of input fields onto model grid)
8331    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
8332       Affects results of exp. rotating_tank ; update output.txt.
8333    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
8334          and taking the square quantity and/or using a fraction-weight field.
8335    o fix aim_diagnostics_init.F mate numbers.
8336    o add mnc output capability to diagnostics/diagstat and update
8337      our cvsignore files for the ACSII output generated
8338    
8339    checkpoint57k_post (2005/07/02)
8340    o lab_sea now uses diagnostics package and provides a suite of
8341      new EXF diagnostics output.
8342    
8343    checkpoint57j_post (2005/06/30)
8344    o exf
8345      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
8346        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
8347        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
8348      * extended diagnostics output
8349        - now includes all EXF variables
8350        - hs, hl moved to common block
8351        - separate S/R for diagnostics, called after ctrl vector is added
8352        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
8353        - EXFqnet contains true Qnet (i.e. includes qsw)
8354      * updated verif. lab_sea, global_with_exf
8355      * Rearranging hflux (exf_mapfields -> exf_getforcing)
8356        to ensure that diagnostics sees a true EXFqnet
8357    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
8358    o diagnostics pkg: change pointers so that 1 diagnostic can be used
8359      several times with different frequencies.
8360    o mnc-ify the thsice package as requested by Daniel Enderton
8361      - the monitor--MNC output needs work
8362      - many attributes need to be added (most are currently blank)
8363    o mnc-ify theaim_v23 package as requested by Daniel Enderton
8364      - many attributes need to be added (most are currently blank)
8365    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
8366    o add Sadourny like discretization to the 4th.O vorticity advection scheme
8367    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
8368      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
8369         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
8370    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
8371     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
8372    
8373    checkpoint57i_post (2005/06/19)
8374    o Diagnostics package was changed: diagnostic allocation is now deactivated
8375      by setting an empty file name in the namelist (used to be by setting 0 frequency)
8376    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
8377      add 1rst Order upwind vertical Shear.
8378    o add a quick fix for A/B checkpointing in OFFLINE mode
8379    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
8380      end-run around the C/Fortran linking horror in eesup/src/timers.F
8381    o added pkg/runclock: allows user to terminate run based on wall clock
8382    o added non-hydrostatic scaling parameter: nh_am2
8383    o pkg/my82: futile attempt to make results compiler-independent by adding
8384      some "_d 0", etc. no effect.
8385    o for mnc output, fill the 'T' coordinate var with myTime and create a
8386      separate 'iter' variable for iteration count
8387    o pkg/diagnostics:
8388      add new capability: output of Global/Regional & per-level statistics ;
8389      tested against monitor output (including land & thSIce) on various exp.
8390    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
8391    
8392    checkpoint57h_done (2005/05/19)
8393      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
8394      data.diagnostics, data.gchem, data.ptracers) is done.
8395    
8396    o pkg/diagnostics: prepare for Global/Regional statistics.
8397      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
8398    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
8399      and rename it: DIFFERENT_MULTIPLE
8400    
8401    checkpoint57h_post (2005/05/14)
8402    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
8403    o pkg/diagnostics: change output frequency, now in seconds (instead
8404      of Nb of iterations). This requires to change data.diagnostics.
8405    checkpoint57h_pre (2005/05/12)
8406    
8407    o in mnc, let the user create the output dir if both mnc_outdir_date
8408      and mnc_outdir_num are false
8409    o add fflags() to pkg/diagnostics which allows one to specify, on a
8410      per-file basis, the file precision [default behavior is unchanged]
8411    o added diagnostics to pkg/kpp, including computation of mixed layer
8412      depth based on a temperature/density criterion
8413    o updated verification/natl_box to test the new pkg/kpp diagnostics
8414    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
8415    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
8416    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
8417      not mnc -- this mistake was found by JMC and is now corrected
8418    
8419    checkpoint57g_post (2005/04/15)
8420    o add Adams-Bashforth 3rd Order time stepping:
8421      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
8422      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
8423    checkpoint57g_pre (2005/04/15)
8424    
8425    o make lambda[Theta,Salt]ClimRelax spatially varying
8426      (default remains spatially uniform constant based on tau)
8427    o added new control variables
8428      * init. uVel, vVel, etanN
8429      * lambda[Theta,Salt]ClimRelax
8430    o separate masks used for ctrl_pack/unpack 'from write_grid' output
8431      (suggested by G. Forget)
8432    
8433    checkpoint57f_post (2005/04/06)
8434    o add parameter "baseTime" = model base time = time at iteration zero
8435      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
8436      account for baseTime shift
8437    o move Coriolis arrays from PARAMS.h to GRID.h
8438    checkpoint57f_pre (2005/04/06)
8439    
8440    o mnc-ifying the seaice package
8441    o introduced an alternative length scale calculation for use in the limiting
8442      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
8443    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
8444    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
8445      as well as grad(vort3).  Made it compatible with both approximate form
8446      for the cubed sphere and full form of these gradients.  Added flag
8447      useFullLeith to select between approximate and full form.  
8448    o add "d0" in getcon.F to reduce differences between compilers/platforms
8449      update output.txt of exp. fizhi-gridalt-hs
8450    o change port_rand funtion to allow to set the seed.
8451    o fix obscure MNC bug involving conversion between reals and integers
8452      - it caused no problems with certain (eg. gcc, ifc) compilers but the
8453        new version is now more standards-compliant
8454    o adjoint-related modifications
8455      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
8456      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
8457      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
8458    
8459    checkpoint57e_post (2005/02/28)
8460    o Adding eddy stress controls a la Ferreira et al.
8461    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
8462    
8463    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
8464      update output.txt of exp. fizhi-gridalt-hs
8465    o add more "Z" dimensions and associated coordinate vars to MNC
8466    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
8467    o parameter calendarDumps: when set, approximate months (30-31 days) and years
8468      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
8469      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
8470      months and years.  Requires pkg/cal.
8471    o diagnostics: add pickup functionality
8472      - off by default for backwards compatibility
8473      - current version only uses MDSIO -- MNC will be added
8474    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
8475    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
8476    
8477    checkpoint57d_post (2005/02/11)
8478    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
8479    o modify verification/ideal_2D_oce so that it tests the creation of mnc
8480      output from the diagnostics package
8481    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
8482    o make genmake2 more portable by using ".$FS" instead of ".f" for more
8483      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
8484    o add coordinate variables to the MNC output from the diagnostics package
8485    o change MNC-flags default value: true when useMNC=TRUE
8486    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
8487      the ability (off by default) to read the grid information using MNC
8488    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
8489    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
8490    o do snap-shot diagnostics at the middle of the time-interval (instead of
8491      at the end).
8492    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
8493      new test for AIM with thSIce + slab-ocean
8494    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
8495    o move state variable diagnostics to the beginning of the time step ;
8496      (note: still needs some work specially for snap-shot diagnostics)
8497      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
8498    
8499    checkpoint57c_post (2005/01/27)
8500    o Change testing option (-ieee) to get closer agreement between g77 & ifort
8501    o generate new output.txt files on faulks with g77 & the new -ieee option
8502    checkpoint57c_pre (2005/01/27)
8503    
8504    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
8505      update output.txt of exp. global_ocean.90x40x15
8506    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
8507      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
8508    o add saltFlux(+File) forcing capability with periodicExternalForcing
8509    o allow to use pkg diagnostics for GM-Redi & ThSIce output
8510    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
8511    o improvements for the MNC output from DIAGNOSTICS:
8512      - correct handling of the unlimitied dimension
8513      - all dims now have associated coordinate variables
8514      - variables located at U, V, and Corner ("Z") points are now written
8515        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
8516        *all* data points are output
8517    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
8518    o added pkg/seaice/seaice_monitor.F
8519    o mdsio_readfield.F can now read files visible only to master MPI process.
8520    o pkg/seaice: some test code for ice-modified ocean stress
8521    o exf_getffields interpolation defaults to bilinear for all scalar forcing
8522      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
8523      spurious negative numbers for precipitation and humidity.  Will cause
8524      some small numerical differences for integrations using pkg/exf/exf_interp.F.
8525    o pkg/ctrl/
8526      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
8527        May be enabled via doPackDiag
8528      *  introduce z-scaling of
8529         + gradient (doZscalePack) and
8530         + control (doZscaleUnpack)
8531    o pkg/mdsio/
8532      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
8533      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
8534    
8535    checkpoint57b_post (2004/12/20)
8536    o simplify options in diagnostics_fill arguments (remove weird combinations)
8537    o fix MNC coordinate variables so that they now contain per-face index
8538      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
8539      general, EXCH2 grids are only aligned to a "local" coordinate system
8540    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
8541    o Implement instantaneous output within pkg diagnostics:
8542      setting a negative frequency in data.diagnostics produces
8543     "snap-shot" output (as opposed to time-average if freq > 0)
8544    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
8545      NOTE: change ptracer diagnostics name: use 2 characters to work with
8546            more than 9 tracers. Add also diagnostics of advect & diffus flux.
8547    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
8548      becomes the coordinate variable for the 'T' dimension
8549    o add CF-style coordinate variables to MNC
8550      - just a first cut:  numbers are meaningless on the cubesphere and
8551        missing along the T axis but otherwise it works!
8552    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
8553    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
8554    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
8555      this is based directly on what the model compute, so that the content of
8556      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
8557    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
8558    o clean up build options files for SunOS, in particular
8559      - remove -traditional from xmakedepend
8560      - change -xarch=v9 to -xarch=native for f77
8561      - restore use of make (not gmake)
8562      - add CC=gcc if using g77
8563    o changes per discussion of AM, JMC, & EH3 today:
8564      - move redundant "grid" variables out of "state" -- in preparation of
8565        creating proper CF-style coordinate variables and in recognition
8566        that any/all grid variables can be easily copied (eg. w/NCO) from
8567        the grid files into any of the other NetCDF files
8568      - *always* output grid variables with MDSIO (this will eventually be
8569        changed)
8570      - output MNC grid file if useMNC is true
8571    o every instance of _END_MASTER() has been found and replaced with
8572      _END_MASTER( myThid ) in order to satisfy certain picky Sun
8573      preprocessors
8574    o re-arrange diagnostics pkg initialisation:
8575     - allow each package to extend the available diagnostics list
8576     - add some checking and fix small problems (multi-threaded, ...)
8577     - new S/R diagnostics_fill (replace fill_diagnostics):
8578       look through the short list of active diag. (instead of the long list)
8579       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
8580    
8581    checkpoint57a_post (2004/12/10)
8582    o this set of changes restores TAMC compatibility
8583      tested for global_ocean.90x40x15 adjoint on trough
8584      (what a pain)
8585    
8586    checkpoint57a_pre (2004/12/10)
8587    o some modifs in tools/build_options for sunos
8588    o call ctrl_pack for ctrl at end for optimcycle=0
8589    
8590    checkpoint57 (2004/12/09)
8591    o add horizontal bi-harmonic viscosity for vertical velocity
8592      - new parameter viscA4W (defaults to viscA4)
8593      - affects only non-hydrostatic code
8594      - to be done: no-slip lateral boundary conditions
8595    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
8596    o implement Implicit Vertical advection for pTracers
8597  o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)  o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
8598    (implemented also for implicit vertical diffusion & advection)    (implemented also for implicit vertical diffusion & advection)
8599  o OBCS: extend application of tracer open boundary conditions  o OBCS: extend application of tracer open boundary conditions
# Line 11  o add call monitor to TAF set of require Line 8602  o add call monitor to TAF set of require
8602    and include in natl_box_adjoint    and include in natl_box_adjoint
8603  o untangle a few ifdefs related to cost, ctrl, autodiff  o untangle a few ifdefs related to cost, ctrl, autodiff
8604    untangel a few ALLOW_ECCO_OPTIMIZATION    untangel a few ALLOW_ECCO_OPTIMIZATION
8605    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
8606      (theta2, salt2 in ecco_cost_weights)
8607    
8608  checkpoint56c_post  checkpoint56c_post (2004/12/03)
8609  o OBCS as control variables  o OBCS as control variables
8610    - update ctrl_ad_diff.list, obcs_ad_diff.list    - update ctrl_ad_diff.list, obcs_ad_diff.list
8611    - remove balance of obcs controls from default    - remove balance of obcs controls from default
# Line 30  o exf: Line 8623  o exf:
8623  o mdsio:  o mdsio:
8624    - i/o-vector change debugLevel from debLevA to debLevB    - i/o-vector change debugLevel from debLevA to debLevB
8625    
8626  checkpoint56b_post  checkpoint56b_post (2004/12/01)
8627  o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that  o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
8628    is called from DO_THE_MODEL_IO    is called from DO_THE_MODEL_IO
8629    - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE    - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
# Line 45  o testreport previously did a lousy job Line 8638  o testreport previously did a lousy job
8638    testreport.    testreport.
8639  o ptracers_monitor: bug fix for MPI  o ptracers_monitor: bug fix for MPI
8640    
8641  checkpoint56a_post  checkpoint56a_post (2004/11/28)
8642  o GCHEM: finish reorganizating the package  o GCHEM: finish reorganizating the package
8643    - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency    - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
8644      (introduces another 3D-array for each passive tracer, but only if      (introduces another 3D-array for each passive tracer, but only if
# Line 90  o GCHEM: Line 8683  o GCHEM:
8683    - cleaning up    - cleaning up
8684  o small cleaning of exch2: remove files that are also in eesupp/src  o small cleaning of exch2: remove files that are also in eesupp/src
8685    
8686  checkpoint56  checkpoint56 (2004/11/17)
8687  o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0  o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
8688  o mnc: cleanup "full" files--fixes out-of-memory problem  o mnc: cleanup "full" files--fixes out-of-memory problem
8689  o ECCO-GODAE  o ECCO-GODAE
# Line 120  o mdsio: filename info to both stderr, s Line 8713  o mdsio: filename info to both stderr, s
8713  o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]  o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
8714    from sign change    from sign change
8715    
8716  checkpoint55j_post  checkpoint55j_post (2004/11/10)
8717  o isolate dissipation tendency (allow to keep it out off AB) in V.I form.  o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
8718    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
8719  o add consistent build directories and .cvsignore files to verification  o add consistent build directories and .cvsignore files to verification
# Line 131  o make all subroutines 30 or less charac Line 8724  o make all subroutines 30 or less charac
8724  o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;  o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
8725    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
8726    
8727  checkpoint55i_post  checkpoint55i_post (2004/10/28)
8728  o change arrays for total vertical diffusivity (2.D if explicit,  o change arrays for total vertical diffusivity (2.D if explicit,
8729    3.D if implicit) ; each ptracer uses its own background value.    3.D if implicit) ; each ptracer uses its own background value.
8730  o added mnc/NetCDF output capability to ocn_compon_interf  o added mnc/NetCDF output capability to ocn_compon_interf
# Line 146  o give MNC the ability to create additio Line 8739  o give MNC the ability to create additio
8739  o Compute the non-local term using either KPP vertical diffusivity (=default)  o Compute the non-local term using either KPP vertical diffusivity (=default)
8740     or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)     or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
8741    
8742  checkpoint55h_post  checkpoint55h_post (2004/10/20)
8743  o add verification test "vermix"  o add verification test "vermix"
8744  o remove all the *_ioinc flags and replace with the single global  o remove all the *_ioinc flags and replace with the single global
8745    outputTypesInclusive flag    outputTypesInclusive flag
# Line 154  o allow to set a vertical profile of ver Line 8747  o allow to set a vertical profile of ver
8747  o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS  o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
8748  o useMNC moved from data.mnc to data.pkg  o useMNC moved from data.mnc to data.pkg
8749    
8750  checkpoint55g_post  checkpoint55g_post (2004/10/14)
8751  o Renaming carbon AD experiments to comply with testreport conventions  o Renaming carbon AD experiments to comply with testreport conventions
8752  o Updating adjoint of Held-Suarez hs94.1x64x5  o Updating adjoint of Held-Suarez hs94.1x64x5
8753  o Fixing directives for non-ECCO forward_step, after ECCO directives  o Fixing directives for non-ECCO forward_step, after ECCO directives
# Line 164  o Fixing directives for non-ECCO forward Line 8757  o Fixing directives for non-ECCO forward
8757  o Updating adjoint output for natl_box_adjoint after  o Updating adjoint output for natl_box_adjoint after
8758    pkg/ecco has been modified (see taga c55d_post)    pkg/ecco has been modified (see taga c55d_post)
8759    
8760  checkpoint55f_post  checkpoint55f_post (2004/10/13)
8761  o rename to timeave_init_fixed  o rename to timeave_init_fixed
8762    
8763  checkpoint55e_post  checkpoint55e_post (2004/10/13)
8764  o some delicate re-shuffle of store directives to avoid one  o some delicate re-shuffle of store directives to avoid one
8765    extra call of do_oceanic_physics    extra call of do_oceanic_physics
8766    affects ecco_the_main_loop.F, do_oceanic_physics.F    affects ecco_the_main_loop.F, do_oceanic_physics.F
# Line 175  o some delicate re-shuffle of store dire Line 8768  o some delicate re-shuffle of store dire
8768  o NB: this may break global_ocean adjoint temporarily,  o NB: this may break global_ocean adjoint temporarily,
8769    but it is clear how to fix it. Will do later, need this now.    but it is clear how to fix it. Will do later, need this now.
8770    
8771  checkpoint55d_post  checkpoint55d_post (2004/10/11)
8772  o ECCO specific cost function terms (up-to-date with 1x1 runs)  o ECCO specific cost function terms (up-to-date with 1x1 runs)
8773  o ecco_cost_weights is modified to 1x1 runs  o ecco_cost_weights is modified to 1x1 runs
8774  o modifs to allow observations to be read in as  o modifs to allow observations to be read in as
8775    single file or yearly files    single file or yearly files
8776  o enable to read exf forcing fields as either  o enable to read exf forcing fields as either
8777    single file or yearly files (flag useExfYearlyFields)    single file or yearly files (flag useExfYearlyFields)
8778  checkpoint55d_pre  checkpoint55d_pre (2004/10/08)
8779    
8780  o switch between 2-level and 3-level checkpointing  o switch between 2-level and 3-level checkpointing
8781  o add ability of MNC to write local and "partial" (eg. 2D slices where  o add ability of MNC to write local and "partial" (eg. 2D slices where
# Line 230  o more obcs stuff Line 8823  o more obcs stuff
8823    - changed argument list of OBCS_CALC to myTime+deltaTclock    - changed argument list of OBCS_CALC to myTime+deltaTclock
8824    - fixed about 35 bugs in obcs_external_fields_load    - fixed about 35 bugs in obcs_external_fields_load
8825    
8826  checkpoint55c_post  checkpoint55c_post (2004/09/23)
8827  o obcs stuff  o obcs stuff
8828    - new runtime flags useOBCSprescribe, useOBCSbalance    - new runtime flags useOBCSprescribe, useOBCSbalance
8829    - re-arranged obcs_calc    - re-arranged obcs_calc
# Line 244  o obcs stuff Line 8837  o obcs stuff
8837  o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments  o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
8838    which simplifies the calls and passes the ifc check-bounds test    which simplifies the calls and passes the ifc check-bounds test
8839    
8840  checkpoint55b_post  checkpoint55b_post (2004/09/22)
8841  o add a 2D scalar, Z location, exchange_2 routine.  o add a 2D scalar, Z location, exchange_2 routine.
8842  o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows  o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
8843    to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]    to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
# Line 255  o use a more standard discretization for Line 8848  o use a more standard discretization for
8848  o fix gad_advection.F (CubedSphere part), back to version 1.23  o fix gad_advection.F (CubedSphere part), back to version 1.23
8849  o fix bug in mom_vi_del2uv.F (CubedSphere part).  o fix bug in mom_vi_del2uv.F (CubedSphere part).
8850    
8851  checkpoint55a_post  checkpoint55a_post (2004/09/20)
8852  o merged code to  o merged code to
8853    * prescribe/read time-dependent open boundaries    * prescribe/read time-dependent open boundaries
8854      (works in conjunction with exf, cal)      (works in conjunction with exf, cal)
# Line 263  o merged code to Line 8856  o merged code to
8856    * each boundary N/S/E/W now has its own CPP option    * each boundary N/S/E/W now has its own CPP option
8857      (healthy for the adjoint)      (healthy for the adjoint)
8858    
8859  checkpoint55  checkpoint55 (2004/09/17)
8860  o up-to-date adjoint of previous breaks  o up-to-date adjoint of previous breaks
8861    - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix    - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
8862    - global_ocean_ebm: adjoint still needs fix (TLM ok)    - global_ocean_ebm: adjoint still needs fix (TLM ok)
# Line 273  o up-to-date adjoint of previous breaks Line 8866  o up-to-date adjoint of previous breaks
8866  o remove all tr1-related code (ALLOW_PASSIVE_TRACER)  o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
8867    (adjoint stuff still has some tr1 'names', but all use ptracer arrays)    (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
8868    
8869  checkpoint54f_post  checkpoint54f_post (2004/09/16)
8870  o in verification/carbin/ remove experiment related to  o in verification/carbin/ remove experiment related to
8871    ALLOW_PASSIVE_TRACER (array tr1 etc)    ALLOW_PASSIVE_TRACER (array tr1 etc)
8872    code_ad/ input_ad/ results_ad    code_ad/ input_ad/ results_ad
# Line 299  o overhaul of IO so that we now have fla Line 8892  o overhaul of IO so that we now have fla
8892    - numerous small formatting cleanups for ProTeX    - numerous small formatting cleanups for ProTeX
8893  o add version info (via BUILD_INFO.h) to MNC and stdout  o add version info (via BUILD_INFO.h) to MNC and stdout
8894    
8895  checkpoint54e_post  checkpoint54e_post (2004/09/02)
8896  o add two new packages  o add two new packages
8897    - pp81 (Packanowski and Philander, 1981), Richardson number and    - pp81 (Packanowski and Philander, 1981), Richardson number and
8898      stratification dependent mixing      stratification dependent mixing
8899    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
8900    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
8901      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
8902      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
8903  o add offline package  o add offline package
8904  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
8905    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz
8906  o genmake2: add ability to search for C compilers and cleanup test output  o genmake2: add ability to search for C compilers and cleanup test output
8907    - fixes recent SX-6 problems and should help with others (eg. HP-UX)    - fixes recent SX-6 problems and should help with others (eg. HP-UX)
8908    
8909  checkpoint54d_post  checkpoint54d_post (2004/07/27)
8910  o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed  o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
8911  o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,  o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
8912    leading to additional shift by 5 days each year of integration    leading to additional shift by 5 days each year of integration
# Line 329  o fix a bug in Flux deriv. vs Ts (pkg/ai Line 8922  o fix a bug in Flux deriv. vs Ts (pkg/ai
8922  o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")  o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
8923  o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)  o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
8924    
8925  checkpoint54c_post  checkpoint54c_post (2004/07/18)
8926  o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr  o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
8927    this affects (truncation error) output.txt of test-exp:    this affects (truncation error) output.txt of test-exp:
8928     global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box     global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
# Line 340  o define the max number of passive trace Line 8933  o define the max number of passive trace
8933  o start to test mnc routinely in exp0  o start to test mnc routinely in exp0
8934  o add sea-ice loading (sIceLoad) as a new forcing field.  o add sea-ice loading (sIceLoad) as a new forcing field.
8935    
8936  checkpoint54b_post  checkpoint54b_post (2004/07/08)
8937  o add testreport "-j JOBS" option for parallel builds (tested and pretty  o add testreport "-j JOBS" option for parallel builds (tested and pretty
8938     impressive on Altix and Opteron systems)     impressive on Altix and Opteron systems)
8939  o diagnostics can now write NetCDF files through the mnc package  o diagnostics can now write NetCDF files through the mnc package
# Line 350  o staggerTimeStep & NLFS: rescale T & S Line 8943  o staggerTimeStep & NLFS: rescale T & S
8943    affects (truncation error) output of lab_sea & natl_box exp.: updated    affects (truncation error) output of lab_sea & natl_box exp.: updated
8944  o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)  o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
8945    
8946  checkpoint54a_post  checkpoint54a_post (2004/07/06)
8947  o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).  o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
8948  o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)  o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
8949  o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)  o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
8950  o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)  o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
8951    + internal_wave (shift in writing cg2d_ini_res)    + internal_wave (shift in writing cg2d_ini_res)
8952  checkpoint54a_pre  checkpoint54a_pre (2004/07/05)
8953    
8954  o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice  o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
8955    - modified verification/lab_sea and natl_box_adjoint accordingly    - modified verification/lab_sea and natl_box_adjoint accordingly
8956    
8957  checkpoint54  checkpoint54 (2004/07/02)
8958  checkpoint53g_post  checkpoint53g_post (2004/07/02)
8959  o prepare splitting of thermodynamics: store convect.counter in common block  o prepare splitting of thermodynamics: store convect.counter in common block
8960  o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)  o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
8961    output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave    output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
# Line 371  o new parameter "nShapS": allow to treat Line 8964  o new parameter "nShapS": allow to treat
8964  o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)  o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
8965  o restore adjointability  o restore adjointability
8966    
8967  checkpoint53f_post  checkpoint53f_post (2004/06/25)
8968  o modifications that affect AIM experiment results (update output.txt):  o modifications that affect AIM experiment results (update output.txt):
8969    - no advection of S at top interface Nr (pkg/generic_advdiff)    - no advection of S at top interface Nr (pkg/generic_advdiff)
8970    - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)    - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
# Line 384  o merged cylindrical coord configuration Line 8977  o merged cylindrical coord configuration
8977  o added rotating_tank experiment  o added rotating_tank experiment
8978  checkpoint53e_pre  checkpoint53e_pre
8979    
8980  checkpoint53d_post  checkpoint53d_post (2004/06/14)
8981  o faulks upgraded: re-generate output.txt that have changed:  o faulks upgraded: re-generate output.txt that have changed:
8982     global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box     global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
8983  o Added Bryan and Lewis, 1979, vertical diffusivity profile  o Added Bryan and Lewis, 1979, vertical diffusivity profile
# Line 403  o regenerated output for global_ocean_eb Line 8996  o regenerated output for global_ocean_eb
8996  o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation  o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
8997    of mom_common/    of mom_common/
8998    - simple re-arrangement of instructions within computing loop    - simple re-arrangement of instructions within computing loop
8999  checkpoint53d_pre  checkpoint53d_pre (2004/05/21)
9000    
9001  checkpoint53c_post  checkpoint53c_post (2004/05/21)
9002  o new version of coupler for AIM+thSIce and Ocean models  o new version of coupler for AIM+thSIce and Ocean models
9003   - new fields (SSS,h_MixLayer ...) are exchanged through the coupler   - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
9004   - land: change Evaporation of snow   - land: change Evaporation of snow
# Line 422  o Adjoint of EBM package + verification Line 9015  o Adjoint of EBM package + verification
9015    * TLM OK    * TLM OK
9016    * ADM not sufficient accuracy yet (needs further testing)    * ADM not sufficient accuracy yet (needs further testing)
9017    
9018  checkpoint53b_post  checkpoint53b_post (2004/05/14)
9019  o Commiting new energy balance model to repository  o Commiting new energy balance model to repository
9020    * package is pkg/ebm    * package is pkg/ebm
9021    * verif. is verification/global_ocean_ebm    * verif. is verification/global_ocean_ebm
# Line 440  C        Destabilization of the thermoha Line 9033  C        Destabilization of the thermoha
9033  C        by atmospheric eddy transports.  C        by atmospheric eddy transports.
9034  C        J. Climate 7(12), 1870-1882  C        J. Climate 7(12), 1870-1882
9035  o Will need long integration testing.  o Will need long integration testing.
9036  checkpoint53b_pre  checkpoint53b_pre (2004/05/14)
9037    
9038  o created pkg/mom_common in preparation for variable viscosity code  o created pkg/mom_common in preparation for variable viscosity code
9039  o renamed and split ini_mnc_io  o renamed and split ini_mnc_io
# Line 448  o pkg/land: only liquid water can diffus Line 9041  o pkg/land: only liquid water can diffus
9041  o AIM using land: soil wetness availability account for snow  o AIM using land: soil wetness availability account for snow
9042  o added printMapIncludesZeros to EEPARMS namelist  o added printMapIncludesZeros to EEPARMS namelist
9043    
9044  checkpoint53a_post  checkpoint53a_post (2004/05/11)
9045  o restore TAMC compatiility for exf_constants.h  o restore TAMC compatiility for exf_constants.h
9046    (no usage of _d in .h)    (no usage of _d in .h)
9047  o Additional storing in KPP in an attempt to fix  o Additional storing in KPP in an attempt to fix
# Line 461  o Fixed verification/natl_box_adjoint ex Line 9054  o Fixed verification/natl_box_adjoint ex
9054    and hence gives results closer to that of Experiment 2.    and hence gives results closer to that of Experiment 2.
9055    Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.    Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
9056    
9057  checkpoint53  checkpoint53 (2004/05/06)
9058  o stable checkpoint with up to date adjoint  o stable checkpoint with up to date adjoint
9059    TLM tests only run for 1st grdchk at the moment. Its unclear if    TLM tests only run for 1st grdchk at the moment. Its unclear if
9060    this is a code problem or a problem with resetting code for g_    this is a code problem or a problem with resetting code for g_
# Line 471  o stable checkpoint with up to date adjo Line 9064  o stable checkpoint with up to date adjo
9064     o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)     o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
9065       are both still in chaos following their security messes.       are both still in chaos following their security messes.
9066    
9067  checkpoint52n_post  checkpoint52n_post (2004/05/06)
9068  o various build (mostly genmake2) changes including:  o various build (mostly genmake2) changes including:
9069    - ability to build/run more easily within Cygwin and MacOS X    - ability to build/run more easily within Cygwin and MacOS X
9070    - more complicated Makefiles with a stronger dependence on Gnu Make    - more complicated Makefiles with a stronger dependence on Gnu Make
# Line 502  o fix in pkg/thsice: Line 9095  o fix in pkg/thsice:
9095    - maintain snow precipitation unchanged (even if Tsf >=0).    - maintain snow precipitation unchanged (even if Tsf >=0).
9096   both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice   both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
9097    
9098  checkpoint52m_post  checkpoint52m_post (2004/04/18)
9099  o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;  o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
9100    this does not change any of the results, because myIter=0 in swfrac always    this does not change any of the results, because myIter=0 in swfrac always
9101    lead to jwtype=2 (the default anyway), but the call makes little sense    lead to jwtype=2 (the default anyway), but the call makes little sense
# Line 534  o test exp. advect_cs: use the standard Line 9127  o test exp. advect_cs: use the standard
9127  o Added functionality to grdchk:  o Added functionality to grdchk:
9128    pick global i,j,k position (or nearest wet) where to perform check.    pick global i,j,k position (or nearest wet) where to perform check.
9129    
9130  checkpoint52l_post  checkpoint52l_post (2004/03/11)
9131  o new land formulation:  o new land formulation:
9132    a) use ground enthalpy as prognostic variable to ensure exact    a) use ground enthalpy as prognostic variable to ensure exact
9133       energy conservation.       energy conservation.
# Line 545  o aim_v23 modification for new land mode Line 9138  o aim_v23 modification for new land mode
9138    a) Treat separately land / ocean / sea-ice surface fluxes    a) Treat separately land / ocean / sea-ice surface fluxes
9139       to allow implicit computation of land & sea-ice surface temp.       to allow implicit computation of land & sea-ice surface temp.
9140    b) add snow precipitation.    b) add snow precipitation.
9141  checkpoint52l_pre  checkpoint52l_pre (2004/03/11)
9142    
9143  o fix problem (when 1 tile is empty) in min/max monitor.  o fix problem (when 1 tile is empty) in min/max monitor.
9144  o fix bug in timeAve (u,vZetatave in common block)  o fix bug in timeAve (u,vZetatave in common block)
# Line 558  o fix ini_curvilinear_grid ; test CS exp Line 9151  o fix ini_curvilinear_grid ; test CS exp
9151  o aim.5l_cs: modify sea-ice fraction input file ; update output  o aim.5l_cs: modify sea-ice fraction input file ; update output
9152  o exf: Adding simple range check routine for exf fields after read  o exf: Adding simple range check routine for exf fields after read
9153    
9154  checkpoint52k_post  checkpoint52k_post (2004/02/23)
9155  o removed top-level directory "diags"  o removed top-level directory "diags"
9156    - we migrated these functions to pkg/timeave a long time ago    - we migrated these functions to pkg/timeave a long time ago
9157  o fixed bug introduced in pkg/monitor  o fixed bug introduced in pkg/monitor
# Line 571  o set all ...Freq to zero after cost_fin Line 9164  o set all ...Freq to zero after cost_fin
9164    taveFreq, dumpFreq, pChkptFreq    taveFreq, dumpFreq, pChkptFreq
9165  o MAIN and ECCO differentiability restored  o MAIN and ECCO differentiability restored
9166    
9167  checkpoint52j_post  checkpoint52j_post (2004/02/18)
9168  o fix nchklev in tamc.h for global_ocean...  o fix nchklev in tamc.h for global_ocean...
9169  o Bringing flow and store directives up-to-date  o Bringing flow and store directives up-to-date
9170  o Really weird thing!  o Really weird thing!
# Line 579  o Really weird thing! Line 9172  o Really weird thing!
9172    starttime, niter0, instead of mytime, myiter, screws up the adjoint:    starttime, niter0, instead of mytime, myiter, screws up the adjoint:
9173    TAF places a faulty re-call of initialise_varia    TAF places a faulty re-call of initialise_varia
9174    after cost_final call which should not be there!    after cost_final call which should not be there!
9175  checkpoint52j_pre  checkpoint52j_pre (2004/02/03)
9176    
9177  o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and  o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
9178    error messages    error messages
# Line 596  o merged mom_vi_calc_relvort3.F, mom_vi_ Line 9189  o merged mom_vi_calc_relvort3.F, mom_vi_
9189    mon_vort3.F to make exch2 friendly with >1 tile per cube face    mon_vort3.F to make exch2 friendly with >1 tile per cube face
9190  o limit timeave output for hi-res integrations  o limit timeave output for hi-res integrations
9191    
9192  checkpoint52i_post  checkpoint52i_post (2004/01/21)
9193  o removed CPP_EEOPTIONS.h from verification/*/code  o removed CPP_EEOPTIONS.h from verification/*/code
9194  o updated the tiling for global_ocean_pressure  o updated the tiling for global_ocean_pressure
9195  checkpoint52i_pre  checkpoint52i_pre (2004/01/20)
9196    
9197  o update aim.5l_LatLon using the standard aim_v23 pkg (instead of  o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
9198    the old pkg/aim).    the old pkg/aim).
9199    
9200  checkpoint52h_pre  checkpoint52h_pre (2004/01/20)
9201  o shortened offending lines in exch2_send_rx?.template  o shortened offending lines in exch2_send_rx?.template
9202  o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator  o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
9203  o genmake2: add build & execute test for NetCDF code  o genmake2: add build & execute test for NetCDF code
# Line 615  o added temporary hack for sea-ice dynam Line 9208  o added temporary hack for sea-ice dynam
9208    metric terms are ignored and it is assumed that    metric terms are ignored and it is assumed that
9209    there is no sea-ice on cube faces 1, 2, 4, and 5.    there is no sea-ice on cube faces 1, 2, 4, and 5.
9210    
9211  checkpoint52f_post  checkpoint52f_post (2004/01/09)
9212  o added exch2 cube routines to pkg/exch2  o added exch2 cube routines to pkg/exch2
9213  o modified hs94.cs-32x32x5 to use it  o modified hs94.cs-32x32x5 to use it
9214  o added new grid files to hs94.cs-32x32x5  o added new grid files to hs94.cs-32x32x5
9215  checkpoint52f_pre  checkpoint52f_pre (2004/01/07)
9216    
9217  checkpoint52e_post  checkpoint52e_post (2004/01/07)
9218  o first attempt to solve vertical advection (momemtum & T,S) Implicitly  o first attempt to solve vertical advection (momemtum & T,S) Implicitly
9219    for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)    for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
9220  o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)  o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
# Line 629  o step.1 : rewrite (as in MultiDimAdvec) Line 9222  o step.1 : rewrite (as in MultiDimAdvec)
9222  o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.  o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
9223  o update output (gad_calc_rhs.F changes affect truncation error) of exp:  o update output (gad_calc_rhs.F changes affect truncation error) of exp:
9224   front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box   front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
9225  checkpoint52e_pre  checkpoint52e_pre (2004/01/02)
9226    
9227  o fix bug in impldiff when Nr=1 or Nr=2.  o fix bug in impldiff when Nr=1 or Nr=2.
9228  o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt  o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
# Line 640  o added exf_offset_atemp for Celsius to Line 9233  o added exf_offset_atemp for Celsius to
9233  o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024  o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
9234  o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations  o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
9235    
9236  checkpoint52d_post  checkpoint52d_post (2003/12/16)
9237  o re-tiled many expts to allow comparison in multi-processor mode  o re-tiled many expts to allow comparison in multi-processor mode
9238    - updated output accordingly    - updated output accordingly
9239    - changed hs94.128x64x5 to use intial T from file rather than use the    - changed hs94.128x64x5 to use intial T from file rather than use the
# Line 669  o check-in the first version of the coup Line 9262  o check-in the first version of the coup
9262  o new verification experiment, cpl_aim+ocn:  o new verification experiment, cpl_aim+ocn:
9263     coupled ocean - AIM atmosphere on cs32 grid.     coupled ocean - AIM atmosphere on cs32 grid.
9264    
9265  checkpoint52d_pre  checkpoint52d_pre (2003/12/06)
9266  o surface flux time-av diagnostic modified for NLFS & RealFreshWater  o surface flux time-av diagnostic modified for NLFS & RealFreshWater
9267  o add call to AIM pendant S/R in external_forcing & external_fields_load.F  o add call to AIM pendant S/R in external_forcing & external_fields_load.F
9268    
9269  checkpoint52c_post  checkpoint52c_post (2003/11/25)
9270  o Fixing OPTIONS files for use of exf:  o Fixing OPTIONS files for use of exf:
9271    - ALLOW_ECCO not needed    - ALLOW_ECCO not needed
9272    - ECCO_CPPOPTIONS.h should not be included from    - ECCO_CPPOPTIONS.h should not be included from
# Line 687  o Removed all CPP options for cal packag Line 9280  o Removed all CPP options for cal packag
9280  o modified STOREs in GAD_ADVECTION  o modified STOREs in GAD_ADVECTION
9281  o corrected key comp. for passkey  o corrected key comp. for passkey
9282    
9283  checkpoint52b_post  checkpoint52b_post (2003/11/23)
9284  o new version: "thsice" of thermodynamic sea-ice pkg:  o new version: "thsice" of thermodynamic sea-ice pkg:
9285   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
9286   - modify fluxes but do not change theta directly;   - modify fluxes but do not change theta directly;
# Line 695  o new version: "thsice" of thermodynamic Line 9288  o new version: "thsice" of thermodynamic
9288   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
9289     + output_thsice.txt to test thsice & bulk_force pkgs.     + output_thsice.txt to test thsice & bulk_force pkgs.
9290  o put back grid & coriolis monitor output.  o put back grid & coriolis monitor output.
9291  checkpoint52b_pre  checkpoint52b_pre (2003/11/23)
9292    
9293  o call "do_the_model_io" at the beginning (=> dump initial state)  o call "do_the_model_io" at the beginning (=> dump initial state)
9294  o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)  o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
# Line 705  o missing PTRACERS headers in some routi Line 9298  o missing PTRACERS headers in some routi
9298  o default tamc.h in pkg/autodiff supposed to crash  o default tamc.h in pkg/autodiff supposed to crash
9299    to ensure proper customization    to ensure proper customization
9300    
9301  checkpoint52a_post  checkpoint52a_post (2003/11/17)
9302  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
9303    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
9304    - subroutine FREEZE_SURFACE now limits only surface temperature    - subroutine FREEZE_SURFACE now limits only surface temperature
# Line 720  o fix problem with ECCO-related divided Line 9313  o fix problem with ECCO-related divided
9313    snapshot file was missing some ad-variables,    snapshot file was missing some ad-variables,
9314    but no warning issued by TAF    but no warning issued by TAF
9315    
9316  checkpoint52a_pre  checkpoint52a_pre (2003/11/12)
9317  o some bug fixes for #undef REAL4_IS_SLOW  o some bug fixes for #undef REAL4_IS_SLOW
9318    
9319  checkpoint52 = ecco_c52_e35  checkpoint52 = ecco_c52_e35
9320  o after testing adjoints of checkpoint51u_post  o after testing adjoints of checkpoint51u_post
9321    
9322  checkpoint51u_post  checkpoint51u_post (2003/11/06)
9323  o this is the post-merge tag of the ecco-branch  o this is the post-merge tag of the ecco-branch
9324    (needs another clean checkout and re-testing)    (needs another clean checkout and re-testing)
9325  o various natl_box_adjoint configs and results  o various natl_box_adjoint configs and results
# Line 741  o top level routines the_main_loop, forw Line 9334  o top level routines the_main_loop, forw
9334    (new namelist ecco_cost_nml)    (new namelist ecco_cost_nml)
9335  o in ctrl/ cleaned some cross-dependencies and updated CPP options  o in ctrl/ cleaned some cross-dependencies and updated CPP options
9336    
9337  checkpoint51t_post  checkpoint51t_post (2003/11/04)
9338  o this is the pre-merge tag of the ecco-branch  o this is the pre-merge tag of the ecco-branch
9339    
9340  checkpoint51s_post  checkpoint51s_post (2003/11/04)
9341  o cleanup: removed various obsolete #define-s  o cleanup: removed various obsolete #define-s
9342  o pkg/grdchk  o pkg/grdchk
9343    - renamed 'ph-grd 3' to 'grad-res'    - renamed 'ph-grd 3' to 'grad-res'
# Line 753  o pkg/grdchk Line 9346  o pkg/grdchk
9346    - additional high-precision output for testreport    - additional high-precision output for testreport
9347      (grep for 'precision_grdchk_result')      (grep for 'precision_grdchk_result')
9348    
9349  checkpoint51r_post  checkpoint51r_post (2003/11/03)
9350  o cleaned up or removed CPP_OPTIONS.h files  o cleaned up or removed CPP_OPTIONS.h files
9351  o updated results for some of the tests to reflect the new  o updated results for some of the tests to reflect the new
9352    optfiles (-ieee: -O0 instead of -O3)    optfiles (-ieee: -O0 instead of -O3)
9353    
9354  checkpoint51q_post  checkpoint51q_post (2003/10/30)
9355  o cd_code:  o cd_code:
9356    - moved cd_scheme.F -> cd_code_scheme.F    - moved cd_scheme.F -> cd_code_scheme.F
9357    - separate read_checkpoint from cd_code_ini_vars.F    - separate read_checkpoint from cd_code_ini_vars.F
# Line 774  o ctrl package totally restructured Line 9367  o ctrl package totally restructured
9367    - confined inclusion of AD_CONFIG.h to where necessary.    - confined inclusion of AD_CONFIG.h to where necessary.
9368  o genmake2: changed AD dependencies from SRCFILES to AD_FILES  o genmake2: changed AD dependencies from SRCFILES to AD_FILES
9369    
9370  checkpoint51p_post  checkpoint51p_post (2003/10/30)
9371  o create initial cd_code package  o create initial cd_code package
9372    - WARNING: the initialization of fields within packages    - WARNING: the initialization of fields within packages
9373      is broken because INI_FIELDS (where READ_CHECKPOINT is      is broken because INI_FIELDS (where READ_CHECKPOINT is
# Line 789  o create initial cd_code package Line 9382  o create initial cd_code package
9382  o cleanup verification/*/code/GMREDI_OPTIONS.h  o cleanup verification/*/code/GMREDI_OPTIONS.h
9383  o cleanup testreport  o cleanup testreport
9384    
9385  checkpoint51o_post  checkpoint51o_post (2003/10/27)
9386  o bringing AD-related verif's up to date with genmake2  o bringing AD-related verif's up to date with genmake2
9387    - carbon/    - carbon/
9388    - global_ocean.90x40x15/    - global_ocean.90x40x15/
# Line 810  o Correcting initialisations for fVerU, Line 9403  o Correcting initialisations for fVerU,
9403  o helping TAF to recognize dependency on kUp for  o helping TAF to recognize dependency on kUp for
9404    fVerU, fVerV    fVerU, fVerV
9405  o Replacing delZ by delR in pkg/ctrl/  o Replacing delZ by delR in pkg/ctrl/
9406  checkpoint51o_pre  checkpoint51o_pre (2003/10/24)
9407    
9408  o undid all of cp51 pending some cleanups and discussion  o undid all of cp51 pending some cleanups and discussion
9409  o added the [#include "AD_CONFIG.h"] statement to all files that need  o added the [#include "AD_CONFIG.h"] statement to all files that need
# Line 818  o added the [#include "AD_CONFIG.h"] sta Line 9411  o added the [#include "AD_CONFIG.h"] sta
9411   o re-worked the build logic in genmake2 to support AD_CONFIG.h   o re-worked the build logic in genmake2 to support AD_CONFIG.h
9412   o removed tools/genmake since it no longer works   o removed tools/genmake since it no longer works
9413    
9414  checkpoint51n_post  checkpoint51n_post (2003/10/23)
9415  o modifications to make FREEZE flux visible to pkg/kpp  o modifications to make FREEZE flux visible to pkg/kpp
9416    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
9417    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
# Line 827  o modifications to make FREEZE flux visi Line 9420  o modifications to make FREEZE flux visi
9420       global_ocean.cs32x15, and global_with_exf)       global_ocean.cs32x15, and global_with_exf)
9421  o added surface flux output variables to TIMEAVE_STATVARS  o added surface flux output variables to TIMEAVE_STATVARS
9422    
9423  checkpoint51n_pre  checkpoint51n_pre (2003/10/23)
9424  o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F  o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
9425  o added [#include "AD_CONFIG.h"] to all files that use the following  o added [#include "AD_CONFIG.h"] to all files that use the following
9426    defines:    defines:
# Line 835  o added [#include "AD_CONFIG.h"] to all Line 9428  o added [#include "AD_CONFIG.h"] to all
9428    - ALLOW_TANGENTLINEAR_RUN    - ALLOW_TANGENTLINEAR_RUN
9429    - ALLOW_ECCO_OPTIMIZATION    - ALLOW_ECCO_OPTIMIZATION
9430    
9431  checkpoint51m_post  checkpoint51m_post (2003/10/21)
9432  o incorporating changes to get TAMC/TAF working in genmake2  o incorporating changes to get TAMC/TAF working in genmake2
9433    - added new TAMC/TAF targets to the Makefile    - added new TAMC/TAF targets to the Makefile
9434    - various cleanups related to package handling    - various cleanups related to package handling
9435    - these changes should have no impact on the forward model    - these changes should have no impact on the forward model
9436    
9437  checkpoint51l_post  checkpoint51l_post (2003/10/20)
9438  o changes to pkg/cal and pkg/exf that allow and speed-up long integrations  o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
9439   - faster algorithm for cal_addtime.F   - faster algorithm for cal_addtime.F
9440   - higher precision arithmetic, where needed   - higher precision arithmetic, where needed
9441   - pkg/exf *startdate variables changed from calendar date to   - pkg/exf *startdate variables changed from calendar date to
9442     model integration time     model integration time
9443    
9444  checkpoint51l_pre  checkpoint51l_pre (2003/10/17)
9445  o add salt flux to forcing fields (used when salty sea-ice forms or melts)  o add salt flux to forcing fields (used when salty sea-ice forms or melts)
9446  o enable to apply restoring on S & T only in a latitude band.  o enable to apply restoring on S & T only in a latitude band.
9447  o update output (external_forcing_surf modif. change truncation errors)  o update output (external_forcing_surf modif. change truncation errors)
9448     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
9449    
9450  checkpoint51k_post  checkpoint51k_post (2003/10/16)
9451  o change default to: useNHMTerms=.FALSE.  o change default to: useNHMTerms=.FALSE.
9452   - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):   - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
9453     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
# Line 868  o added an include barrier to the defaul Line 9461  o added an include barrier to the defaul
9461    removed the #include "PACKAGES_CONFIG.h" from it    removed the #include "PACKAGES_CONFIG.h" from it
9462  o fix a bug in mom_fluxform (from chk51j_post)  o fix a bug in mom_fluxform (from chk51j_post)
9463    
9464  checkpoint51j_post  checkpoint51j_post (2003/10/10)
9465  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
9466  o adjusted some flow directives (dynamics, thermodynamics)  o adjusted some flow directives (dynamics, thermodynamics)
9467  o added cubed-sphere case to test cost function  o added cubed-sphere case to test cost function
# Line 882  o Moving pkg-specific flow directives to Line 9475  o Moving pkg-specific flow directives to
9475         - pkg_ad_diff.list         - pkg_ad_diff.list
9476         - pkg_ad_check_lev?_dir.h         - pkg_ad_check_lev?_dir.h
9477    
9478  checkpoint51i_post  checkpoint51i_post (2003/10/09)
9479  o merge of the branch-genmake2  o merge of the branch-genmake2
9480    - knowingly breaks the older genmake    - knowingly breaks the older genmake
9481    - automatic generation of all ALLOW_${PKG_NAME} defines    - automatic generation of all ALLOW_${PKG_NAME} defines
9482    - new testreport supersedes older testscript    - new testreport supersedes older testscript
9483  o large number of package inclusion and header cleanups  o large number of package inclusion and header cleanups
9484  checkpoint51i_pre  checkpoint51i_pre (2003/10/08)
9485    
9486  o new output for adjoin of global ocean vector invariant  o new output for adjoin of global ocean vector invariant
9487  o fix for checkpoint of thermodynamic seaice and bulk_force  o fix for checkpoint of thermodynamic seaice and bulk_force
# Line 900  o modify gchem pkg to be more versatile Line 9493  o modify gchem pkg to be more versatile
9493  o modifications to clean up dic pkg  o modifications to clean up dic pkg
9494  o add pkg/cfc  o add pkg/cfc
9495    
9496  checkpoint51g_post  checkpoint51g_post (2003/10/02)
9497  o provide links for ARPACK and ADM*TLM  o provide links for ARPACK and ADM*TLM
9498  o start removing verification/vero/  o start removing verification/vero/
9499  o update AD-related stuff  o update AD-related stuff
# Line 908  o update AD-related stuff Line 9501  o update AD-related stuff
9501  o adding to verification/global_ocean.90x40x15/ adjoint of  o adding to verification/global_ocean.90x40x15/ adjoint of
9502    vector invariant setup    vector invariant setup
9503    
9504  checkpoint51f_post  checkpoint51f_post (2003/10/02)
9505  o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)  o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
9506  o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation  o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
9507    of tracer Green's fucntions for ocean inversion project.    of tracer Green's fucntions for ocean inversion project.
9508    
9509  checkpoint51f_pre  checkpoint51f_pre (2003/08/07)
9510  o Added on-the-fly spatial interpolation capability  o Added on-the-fly spatial interpolation capability
9511      "USE_EXF_INTERPOLATION" to pkg/exf.      "USE_EXF_INTERPOLATION" to pkg/exf.
9512    - This is a temporary Cartesian-grid hack until    - This is a temporary Cartesian-grid hack until
# Line 925  o Bug fix to pkg/ptracers, pkg/generic_a Line 9518  o Bug fix to pkg/ptracers, pkg/generic_a
9518      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
9519      non-local transport term.      non-local transport term.
9520    
9521  checkpoint51e_post  checkpoint51e_post (2003/08/03)
9522  o pkg/mom_vecinv:  o pkg/mom_vecinv:
9523    - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)    - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
9524    - add time-ave diagnostic of vorticity advection.    - add time-ave diagnostic of vorticity advection.
# Line 935  o atmospheric geopotential: - include wa Line 9528  o atmospheric geopotential: - include wa
9528  o land pkg: read initial state from files.  o land pkg: read initial state from files.
9529  o AIM : add stratospheric drag in the upper level  o AIM : add stratospheric drag in the upper level
9530    
9531  checkpoint51d_post  checkpoint51d_post (2003/07/18)
9532  o change function ILNBLNK (=> last non-blank char.) to return zero  o change function ILNBLNK (=> last non-blank char.) to return zero
9533    (instead of the string length) when the string. char is empty    (instead of the string length) when the string. char is empty
9534  o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)  o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
# Line 948  o Use cluster local disks for purely loc Line 9541  o Use cluster local disks for purely loc
9541    - new active_file_loc... and mdsio_..._loc routines    - new active_file_loc... and mdsio_..._loc routines
9542    - affected packages: autodiff, ctrl, grdchk, mdsio    - affected packages: autodiff, ctrl, grdchk, mdsio
9543    
9544  checkpoint51c_post  checkpoint51c_post (2003/07/08)
9545  o introducing integer flag debugLevel  o introducing integer flag debugLevel
9546    - debLevZero: suppress all output    - debLevZero: suppress all output
9547    - debLevA: standard    - debLevA: standard
# Line 971  o added verification for adjoint with pt Line 9564  o added verification for adjoint with pt
9564    - checked tapelev/comlev recomputations: OK    - checked tapelev/comlev recomputations: OK
9565  <<<checkpoint51b_pre  <<<checkpoint51b_pre
9566    
9567  checkpoint51a_post  checkpoint51a_post (2003/06/25)
9568  o added code for biogeochemistry package  o added code for biogeochemistry package
9569    - new pkgs: dic, gchem    - new pkgs: dic, gchem
9570    - new subroutine in ptracers    - new subroutine in ptracers
9571  o modify code for biogeo packages  o modify code for biogeo packages
9572    - in model/src and pkg/ptracers    - in model/src and pkg/ptracers
9573    
9574  checkpoint51  checkpoint51 (2003/06/24)
9575  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
9576    - autodiff, ctrl, exf, grdchk, seaice    - autodiff, ctrl, exf, grdchk, seaice
9577    kept separate packages    kept separate packages
# Line 986  o merged improved packages from ecco-bra Line 9579  o merged improved packages from ecco-bra
9579  o updating verification/internal_wave, verification/lab_sea  o updating verification/internal_wave, verification/lab_sea
9580    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
9581    
9582  checkpoint50i_post  checkpoint50i_post (2003/06/23)
9583  o Preparing next differentiable checkpoint and sync  o Preparing next differentiable checkpoint and sync
9584    of MAIN vs. ecco-branch    of MAIN vs. ecco-branch
9585    - 1st step: this one is differentiable    - 1st step: this one is differentiable
9586    - 2nd step: next(! not this) checkpoint will have updated packages    - 2nd step: next(! not this) checkpoint will have updated packages
9587                from ecco-branch)                from ecco-branch)
9588    
9589  checkpoint50h_post  checkpoint50h_post (2003/06/20)
9590  o new package "land": provide surface BC for AIM.  o new package "land": provide surface BC for AIM.
9591  o pkg/ptracers: apply exchange to all tracers after reading a pickup.  o pkg/ptracers: apply exchange to all tracers after reading a pickup.
9592  o AIM: use true log-P extrapolation for near surface temp (= as in  o AIM: use true log-P extrapolation for near surface temp (= as in
# Line 1002  o New variable in PARM03 for more flexib Line 9595  o New variable in PARM03 for more flexib
9595  o somewhat cleaned package initialisation sequence for  o somewhat cleaned package initialisation sequence for
9596    ctrl/ cost/ ecco/ in packages_... routines    ctrl/ cost/ ecco/ in packages_... routines
9597    
9598  checkpoint50g_post  checkpoint50g_post (2003/05/23)
9599  o merged with release1_p17 (pkg/seaice and verification/lab_sea)  o merged with release1_p17 (pkg/seaice and verification/lab_sea)
9600    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
9601    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
9602      made the default because of faster convergence than ADI      made the default because of faster convergence than ADI
9603    
9604  checkpoint50f_post  checkpoint50f_post (2003/05/23)
9605  o exf totally restructured  o exf totally restructured
9606    - replaced all exf_set_ routines by one generic exf_set_gen.F    - replaced all exf_set_ routines by one generic exf_set_gen.F
9607      and made sure it's still differentiable      and made sure it's still differentiable
# Line 1016  o exf totally restructured Line 9609  o exf totally restructured
9609    - exf_inscal_/exf_outscal_ suffixes consistent with field names    - exf_inscal_/exf_outscal_ suffixes consistent with field names
9610    - updated adjoint/makefile and relevant verif. accordingly    - updated adjoint/makefile and relevant verif. accordingly
9611    
9612  checkpoint50f_pre  checkpoint50f_pre (2003/05/23)
9613   o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;   o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
9614        + change Evap over land. (update aim.5l_cs output)        + change Evap over land. (update aim.5l_cs output)
9615   o added missing .cvsignores and made uniform across expts   o added missing .cvsignores and made uniform across expts
# Line 1026  checkpoint50f_pre Line 9619  checkpoint50f_pre
9619   o new fn in pkg/monitor to stop model if solution grows too big   o new fn in pkg/monitor to stop model if solution grows too big
9620   o removed lots of single quotes from comments   o removed lots of single quotes from comments
9621    
9622  checkpoint50e_post  checkpoint50e_post (2003/05/14)
9623  o make KPP work with PTRACERS  o make KPP work with PTRACERS
9624   - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is   - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
9625     nearly a copy of kpp_transport_s     nearly a copy of kpp_transport_s
9626   - there is no analogue to SurfaceTendencyS, so I have to use   - there is no analogue to SurfaceTendencyS, so I have to use
9627     gPtr(of the surface layer) instead     gPtr(of the surface layer) instead
9628  o add a new platform SunFire+mpi (SunFire 15000) to genmake  o add a new platform SunFire+mpi (SunFire 15000) to genmake
9629  checkpoint50e_pre  checkpoint50e_pre (2003/05/13)
9630    
9631  checkpoint50d_post  checkpoint50d_post (2003/05/13)
9632  o change kpp output from multiple-record state files to single-record state  o change kpp output from multiple-record state files to single-record state
9633    files analogous to write_state.F    files analogous to write_state.F
9634  o reduce the output frequency of cg3d-related stuff to the monitor frequency,  o reduce the output frequency of cg3d-related stuff to the monitor frequency,
9635    analogous to the cg2d-related output.    analogous to the cg2d-related output.
9636  o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,  o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
9637    so that writing to internal file fn (with length 512) fails.    so that writing to internal file fn (with length 512) fails.
9638  checkpoint50d_pre  checkpoint50d_pre (2003/05/12)
9639    
9640  checkpoint50c_post  checkpoint50c_post (2003/05/12)
9641  o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)  o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
9642  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
9643  o add time-average diagnostic of U*V and vertical diffusive flux for theta.  o add time-average diagnostic of U*V and vertical diffusive flux for theta.
9644  o bug fixed in convective adjustment diagnostic (multi-tile set-up).  o bug fixed in convective adjustment diagnostic (multi-tile set-up).
9645  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
9646    
9647  checkpoint50c_pre  checkpoint50c_pre (2003/04/30)
9648  Merging from release1_p13:  Merging from release1_p13:
9649  o bug fix for pkg/seaice dynamic solver  o bug fix for pkg/seaice dynamic solver
9650  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
9651    
9652  checkpoint50b_post  checkpoint50b_post (2003/04/17)
9653  o store u*,v* in gU,V instead of in guNm1,gvNm1  o store u*,v* in gU,V instead of in guNm1,gvNm1
9654  o in order to put the momForcing out of the Adams-Bashforth:  o in order to put the momForcing out of the Adams-Bashforth:
9655    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
# Line 1065  o new flag "useCDscheme" (default=F); re Line 9658  o new flag "useCDscheme" (default=F); re
9658  o re-generate output for highly sensitive test-exp:  o re-generate output for highly sensitive test-exp:
9659     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
9660    
9661  checkpoint50b_pre  checkpoint50b_pre (2003/04/17)
9662  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
9663  o corrected CPP option mismatch in exf_Bulk... functions for case  o corrected CPP option mismatch in exf_Bulk... functions for case
9664    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
9665    
9666  checkpoint50a_post  checkpoint50a_post (2003/03/21)
9667  o Bug fix for merging between c50 and KPP.  o Bug fix for merging between c50 and KPP.
9668    ikey was passed from thermodynamics to kpp_calc via    ikey was passed from thermodynamics to kpp_calc via
9669    common block rather than being recomputed in kpp_calc,    common block rather than being recomputed in kpp_calc,
9670    in contradiction with new key itdkey.    in contradiction with new key itdkey.
9671    New key ikppkey created, and tamc.h headers updated.    New key ikppkey created, and tamc.h headers updated.
9672    
9673  checkpoint50  checkpoint50 (2003/03/08)
9674  - 2nd step of merge with ecco-branch:  - 2nd step of merge with ecco-branch:
9675    merge changes in ecco-branch back into main trunk    merge changes in ecco-branch back into main trunk
9676  - bug fix in find_alpha  - bug fix in find_alpha
# Line 1085  checkpoint50 Line 9678  checkpoint50
9678  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
9679  - merged some sliced AD support routines  - merged some sliced AD support routines
9680    
9681  checkpoint49  checkpoint49 (2003/03/06)
9682  merged from ecco-branch:  merged from ecco-branch:
9683  o exf:  o exf:
9684    - Enable initialisation of forcing fields to constant    - Enable initialisation of forcing fields to constant
# Line 1123  o DIVA: Line 9716  o DIVA:
9716    (see MITgcm manual).    (see MITgcm manual).
9717  o cal: synchronized between MAIN and ecco-branch  o cal: synchronized between MAIN and ecco-branch
9718    
9719  checkpoint48i_post  checkpoint48i_post (2003/03/05)
9720  o Changes to restore differentiability of code w.r.t. previous tag  o Changes to restore differentiability of code w.r.t. previous tag
9721    (mostly adding new routines to make list and replacing    (mostly adding new routines to make list and replacing
9722    pressure by totPhiHyd).    pressure by totPhiHyd).
# Line 1141  o Modif. for DIVA: Line 9734  o Modif. for DIVA:
9734    tbar, sbar, psbar, which should not be reinitialised;    tbar, sbar, psbar, which should not be reinitialised;
9735    only relevant for ecco-branch)    only relevant for ecco-branch)
9736    
9737  checkpoint48h_post  checkpoint48h_post (2003/02/28)
9738  o improve "ini_p_ground" when using finite difference form for calc_phi_hyd  o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
9739  o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F  o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
9740  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
9741  o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT  o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
9742    
9743  checkpoint48g_post  checkpoint48g_post (2003/02/18)
9744  --- EOS:  --- EOS:
9745  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
9746    store total Potential in totPhyHyd for diagnostics & EOS.    store total Potential in totPhyHyd for diagnostics & EOS.
# Line 1161  o accurate phiHyd when using interface-W Line 9754  o accurate phiHyd when using interface-W
9754   ( changes results of ideal_2D_oce )   ( changes results of ideal_2D_oce )
9755  o includes r* 2nd term in potential gradient.  o includes r* 2nd term in potential gradient.
9756    
9757  checkpoint48f_post  checkpoint48f_post (2003/02/18)
9758  Merging from release1_p12:  Merging from release1_p12:
9759  o Modifications for using pkg/exf with pkg/seaice  o Modifications for using pkg/exf with pkg/seaice
9760    - improved description of the various forcing configurations    - improved description of the various forcing configurations
# Line 1189  o pkg/seaice: Line 9782  o pkg/seaice:
9782    - adjoint-friendly modifications    - adjoint-friendly modifications
9783    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
9784    
9785  checkpoint48e_post  checkpoint48e_post (2003/02/12)
9786  o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)  o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
9787  o dynamics: change definition of computational domain & adapt mom_fluxform  o dynamics: change definition of computational domain & adapt mom_fluxform
9788    accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.    accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
# Line 1200  o following exp works with Olx=Oly=2 (an Line 9793  o following exp works with Olx=Oly=2 (an
9793      inverted_barometer solid-body.cs-32x32x1      inverted_barometer solid-body.cs-32x32x1
9794    (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)    (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
9795    
9796  checkpoint48d_post  checkpoint48d_post (2003/02/09)
9797  o in preparation for r*:  o in preparation for r*:
9798   a) use pre-computed gradient of hydrostatic potential:   a) use pre-computed gradient of hydrostatic potential:
9799      changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce      changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
# Line 1208  o in preparation for r*: Line 9801  o in preparation for r*:
9801      => affects results of glob_oce_pressure (different truncation error)        => affects results of glob_oce_pressure (different truncation error)  
9802    update output.txt of ideal_2D_oce & global_ocean_pressure    update output.txt of ideal_2D_oce & global_ocean_pressure
9803    
9804  checkpoint48d_pre  checkpoint48d_pre (2003/02/08)
9805  o in preparation for r*:  o in preparation for r*:
9806    new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.    new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
9807    pass the 2 comp. of the grad. as arguments to momentum S/R.    pass the 2 comp. of the grad. as arguments to momentum S/R.
9808    but for the moment, only used if it does not change the results.    but for the moment, only used if it does not change the results.
9809  o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP  o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
9810    
9811  checkpoint48c_post  checkpoint48c_post (2003/02/06)
9812  Modifications in treatment of initial flux forcing controls  Modifications in treatment of initial flux forcing controls
9813  to avoid extra storing of flux fields.  to avoid extra storing of flux fields.
9814    
9815  checkpoint48c_pre  checkpoint48c_pre (2003/01/21)
9816  o Added tidal_basin_2d experiment (currently 1D!)  o Added tidal_basin_2d experiment (currently 1D!)
9817  o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)  o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
9818    
9819  checkpoint48b_post  checkpoint48b_post (2003/01/27)
9820  o r* coordinate added in #ifdef NONLIN_FRSURF block.  o r* coordinate added in #ifdef NONLIN_FRSURF block.
9821   (modification to pressure gradient not yet implemented)   (modification to pressure gradient not yet implemented)
9822  o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports  o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
9823    (for U & V) that are used for vertical advection of momentum.    (for U & V) that are used for vertical advection of momentum.
9824    
9825  checkpoint48a_post  checkpoint48a_post (2003/01/24)
9826  o In preparation for r*, use temp. array to compute vertical transport  o In preparation for r*, use temp. array to compute vertical transport
9827     in flux-form momentum pkg. => change results of few test-exp.     in flux-form momentum pkg. => change results of few test-exp.
9828    Update output of: exp4, exp5, front_relax, global_ocean_pressure,    Update output of: exp4, exp5, front_relax, global_ocean_pressure,
9829                      lab_sea, natl_box & plume_on_slope                      lab_sea, natl_box & plume_on_slope
9830    
9831  checkpoint48  checkpoint48 (2003/01/23)
9832  o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')  o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
9833    
9834  checkpoint47j_post  checkpoint47j_post (2003/01/21)
9835  o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.  o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
9836  o moved adexch from forward_step to addummy_in_stepping  o moved adexch from forward_step to addummy_in_stepping
9837  o added exch in ctrl_map_...  o added exch in ctrl_map_...
# Line 1257  o Yet more changes in gmredi: Line 9850  o Yet more changes in gmredi:
9850      re-activated full calculation of taperfct for case 'ac02'      re-activated full calculation of taperfct for case 'ac02'
9851  o updating verification/ adjoints of carbon, global_ocean.90x40x15  o updating verification/ adjoints of carbon, global_ocean.90x40x15
9852    
9853  checkpoint47i_post  checkpoint47i_post (2003/01/13)
9854  o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.  o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
9855  o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)  o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
9856    default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)    default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
# Line 1273  o case GM_BOLUS_ADVEC should be cleaned Line 9866  o case GM_BOLUS_ADVEC should be cleaned
9866    S/R gmredi_slope_psi should be cleaned    S/R gmredi_slope_psi should be cleaned
9867  o verification/carbon now has exactConserv=.TRUE.  o verification/carbon now has exactConserv=.TRUE.
9868    
9869  checkpoint47g_post  checkpoint47g_post (2003/01/10)
9870  o time-average AIM output: becomes independent from statvars time-average  o time-average AIM output: becomes independent from statvars time-average
9871    (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)    (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
9872  o After TAF bug fix:  o After TAF bug fix:
# Line 1299  Gradient checks OK for Line 9892  Gradient checks OK for
9892  in conjunction with data.gmredi parameters to be checked in  in conjunction with data.gmredi parameters to be checked in
9893  in a few minutes under verification/carbon/code/  in a few minutes under verification/carbon/code/
9894    
9895  checkpoint47f_post  checkpoint47f_post (2002/12/28)
9896  Merging from release1_p10:  Merging from release1_p10:
9897  o modifications for using pkg/exf with pkg/seaice  o modifications for using pkg/exf with pkg/seaice
9898    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
# Line 1311  o modifications for using pkg/exf with p Line 9904  o modifications for using pkg/exf with p
9904    - verification/lab_sea default experiment now uses    - verification/lab_sea default experiment now uses
9905      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
9906    
9907  checkpoint47e_post  checkpoint47e_post (2002/12/27)
9908  o created a tag prior to creating a branch  o created a tag prior to creating a branch
9909    
9910  checkpoint47d_post  checkpoint47d_post (2002/12/16)
9911  o fixed bug in the oceanic pressure coordinates code: vertical viscosity  o fixed bug in the oceanic pressure coordinates code: vertical viscosity
9912    at the bottom boundary had an erroneous half slip boundary condition    at the bottom boundary had an erroneous half slip boundary condition
9913  o added bottom drag and no slip boundary condition capabilities to  o added bottom drag and no slip boundary condition capabilities to
9914    oceanic pressure coordinates code    oceanic pressure coordinates code
9915  o added new verification experiment global_ocean_pressure, this experiment is  o added new verification experiment global_ocean_pressure, this experiment is
9916    also described in the tutorial section of the manual    also described in the tutorial section of the manual
9917  checkpoint47d_pre  checkpoint47d_pre (2002/12/16)
9918    
9919  checkpoint47c_post  checkpoint47c_post (2002/12/16)
9920  o Added a verification experiment for a global cubed-sphere ocean run  o Added a verification experiment for a global cubed-sphere ocean run
9921    -  verification/global_ocean.cubed32x32x30    -  verification/global_ocean.cubed32x32x30
9922    -  uses pkg/therm_seaice and pkg/bulk_forcing    -  uses pkg/therm_seaice and pkg/bulk_forcing
# Line 1335  o OCEANICP & realFreshWater: include P-E Line 9928  o OCEANICP & realFreshWater: include P-E
9928    NOTES: requires option NONLIN_FRSURF to be "#define".    NOTES: requires option NONLIN_FRSURF to be "#define".
9929  o update advect_xz/results/output.txt (left from checkpoint44g_post)  o update advect_xz/results/output.txt (left from checkpoint44g_post)
9930    
9931  checkpoint47b_post  checkpoint47b_post (2002/12/05)
9932  Merging from release1_p9:  Merging from release1_p9:
9933  o pkg/seaice  o pkg/seaice
9934    - removed GOTO's and added taf directives    - removed GOTO's and added taf directives
# Line 1352  o verification/lab_sea Line 9945  o verification/lab_sea
9945    - added missing matlab routines    - added missing matlab routines
9946    - added test of thermodynamics parallelization    - added test of thermodynamics parallelization
9947    
9948  checkpoint47a_post  checkpoint47a_post (2002/11/23)
9949  o new pkg: aim_v23  o new pkg: aim_v23
9950   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
9951     for now, keep the same surface forcing as before.     for now, keep the same surface forcing as before.
# Line 1369  o bulk_force and therm_seaice Line 9962  o bulk_force and therm_seaice
9962  - Two ifdef statements for compile time,  - Two ifdef statements for compile time,
9963     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
9964    
9965  checkpoint47  checkpoint47 (2002/11/15)
9966  differentiable version of checkpoint46n_post  differentiable version of checkpoint46n_post
9967  o bug fix in quasihydrostaticterms  o bug fix in quasihydrostaticterms
9968  o * "clean" adjoint code (in terms of extensive recomputations)  o * "clean" adjoint code (in terms of extensive recomputations)
# Line 1398  o Updated verification/carbon/ Line 9991  o Updated verification/carbon/
9991    - #define GM_VISBECK_VARIABLE_K    - #define GM_VISBECK_VARIABLE_K
9992    - GM_taper_scheme    = 'ldd97'        - GM_taper_scheme    = 'ldd97'    
9993    
9994  checkpoint46n_post  checkpoint46n_post (2002/11/12)
9995  Merging from release1_p8:  Merging from release1_p8:
9996  o verification/natl_box:  o verification/natl_box:
9997    updating new external_fields_load routine    updating new external_fields_load routine
# Line 1452  o Adding new verification experiment glo Line 10045  o Adding new verification experiment glo
10045    the exf (and cal) package instead of the    the exf (and cal) package instead of the
10046    external_fields_load routine (cf README file).    external_fields_load routine (cf README file).
10047    
10048  checkpoint46m_post  checkpoint46m_post (2002/11/07)
10049  o modified testscript to return -- when there are no lines of "%MON" output  o modified testscript to return -- when there are no lines of "%MON" output
10050  o added new flag "quasiHydrostatic" for QH mode  o added new flag "quasiHydrostatic" for QH mode
10051    and new routine quasihydrostaticterms()    and new routine quasihydrostaticterms()
# Line 1465  o introduced flag for controllin non-hyd Line 10058  o introduced flag for controllin non-hyd
10058  o removed gravitySign from PARM04  o removed gravitySign from PARM04
10059  o switched to g77/ifc from pgf77 in aim experiments  o switched to g77/ifc from pgf77 in aim experiments
10060    
10061  checkpoint46l_post  checkpoint46l_post (2002/11/01)
10062  o made convective adjustment work with pressure coordinates:  o made convective adjustment work with pressure coordinates:
10063   - changed the direction of k-loop in convective_adjustment.F for the   - changed the direction of k-loop in convective_adjustment.F for the
10064     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
# Line 1478  o made convective adjustment work with p Line 10071  o made convective adjustment work with p
10071     at the beginning of find_rho, find_alpha, and find_beta, does a     at the beginning of find_rho, find_alpha, and find_beta, does a
10072     check of the entire slice, if CPP-option     check of the entire slice, if CPP-option
10073     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
10074  checkpoint46l_pre  checkpoint46l_pre (2002/10/23)
10075    
10076  checkpoint46k_post  checkpoint46k_post (2002/10/23)
10077  o fixed the verification/global_ocean.90x40x15 experiment:  o fixed the verification/global_ocean.90x40x15 experiment:
10078   - new bathymetry (the world according to A., JMC, and M.)   - new bathymetry (the world according to A., JMC, and M.)
10079   - new initial fields and forcing fields (*.bin files)   - new initial fields and forcing fields (*.bin files)
# Line 1494  o S/R aim_initialise.F replace S/R aim_i Line 10087  o S/R aim_initialise.F replace S/R aim_i
10087   - read AIM physics parameters from a file (data.aimphys)   - read AIM physics parameters from a file (data.aimphys)
10088   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
10089    
10090  checkpoint46j_post  checkpoint46j_post (2002/10/07)
10091  o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH  o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
10092  o move wVel computation at the end of the time step, in S/R integr_continuity  o move wVel computation at the end of the time step, in S/R integr_continuity
10093  o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)  o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
10094  o update timeave pkg for wVel diagnostic.  o update timeave pkg for wVel diagnostic.
10095  checkpoint46j_pre  checkpoint46j_pre (2002/09/27)
10096    
10097  checkpoint46i_post  checkpoint46i_post (2002/09/25)
10098  o Clean up AIM package (and keep the results unchanged):  o Clean up AIM package (and keep the results unchanged):
10099    include CPP_OPTION and use IMPLICT NONE in all routines ;    include CPP_OPTION and use IMPLICT NONE in all routines ;
10100    declare all the variables _RL ; use _d 0 for all numerical constants.    declare all the variables _RL ; use _d 0 for all numerical constants.
10101    use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !    use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
10102    
10103  checkpoint46h_post  checkpoint46h_post (2002/09/25)
10104  o cleaned up the use of rhoNil and rhoConst.  o cleaned up the use of rhoNil and rhoConst.
10105    - rhoNil should only appear in the LINEAR equation of state, everywhere    - rhoNil should only appear in the LINEAR equation of state, everywhere
10106      else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst      else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
# Line 1517  o introduced new parameter rhoConstFresh Line 10110  o introduced new parameter rhoConstFresh
10110    value is 999.8 kg/m^3    value is 999.8 kg/m^3
10111  o cleanup up external_forcing.F and external_forcing_surf.F  o cleanup up external_forcing.F and external_forcing_surf.F
10112    - can now be used by both OCEANIC and OCEANICP    - can now be used by both OCEANIC and OCEANICP
10113  checkpoint46h_pre  checkpoint46h_pre (2002/09/18)
10114    
10115   Added code to convert surface volume flux (fresh water) into   Added code to convert surface volume flux (fresh water) into
10116   a mass flux when using P coordinates in the ocean (OCEANICP).   a mass flux when using P coordinates in the ocean (OCEANICP).
10117   Note: It assumes you have set rho0=rhoConst=density of fresh water.   Note: It assumes you have set rho0=rhoConst=density of fresh water.
10118    
10119  checkpoint46g_post  checkpoint46g_post (2002/09/18)
10120  o Include a new diagnostic variable phiHydLow for the ocean model  o Include a new diagnostic variable phiHydLow for the ocean model
10121    - in z-coordinates, it is the bottom pressure anomaly    - in z-coordinates, it is the bottom pressure anomaly
10122    - in p-coordinates, it is the sea surface elevation    - in p-coordinates, it is the sea surface elevation
# Line 1541  o cleaned up find_rho Line 10134  o cleaned up find_rho
10134    - removed obsolete 'eqn' from the parameter list.    - removed obsolete 'eqn' from the parameter list.
10135  o added two new verification experiments: gop and goz  o added two new verification experiments: gop and goz
10136    (4x4 degree global ocean, 15 layers in pressure and height coordinates)    (4x4 degree global ocean, 15 layers in pressure and height coordinates)
10137  checkpoint46g_pre  checkpoint46g_pre (2002/09/16)
10138    
10139  checkpoint46f_post  checkpoint46f_post (2002/09/16)
10140  o Enable tangent linear (forward mode) gradient checks:  o Enable tangent linear (forward mode) gradient checks:
10141    - extended active file handling to g_... files    - extended active file handling to g_... files
10142    - added TANGENT_SIMULATION to theSimulationMode    - added TANGENT_SIMULATION to theSimulationMode
# Line 1551  o Enable tangent linear (forward mode) g Line 10144  o Enable tangent linear (forward mode) g
10144  o added tangent linear setup in verification/carbon/code_ftl  o added tangent linear setup in verification/carbon/code_ftl
10145  o added adjoint setup in verification/front_relax/code_ad  o added adjoint setup in verification/front_relax/code_ad
10146    
10147  checkpoint46e_post  checkpoint46e_post (2002/09/05)
10148  o Added new equation of state -> MDJWF  o Added new equation of state -> MDJWF
10149    - EOS of McDougall et al., 2002, JAOT, submitted    - EOS of McDougall et al., 2002, JAOT, submitted
10150    - caveat: the equation of state is only valid for a smaller (more    - caveat: the equation of state is only valid for a smaller (more
# Line 1560  o Added new equation of state -> MDJWF Line 10153  o Added new equation of state -> MDJWF
10153    - added more check values for density in check_eos (ini_eos.F), some of    - added more check values for density in check_eos (ini_eos.F), some of
10154      the old check values are out of the range of the MDJWF-eos, so don't      the old check values are out of the range of the MDJWF-eos, so don't
10155      expect perfect matches for those      expect perfect matches for those
10156  checkpoint46e_pre  checkpoint46e_pre (2002/08/19)
10157    
10158  checkpoint46d_post  checkpoint46d_post (2002/08/19)
10159  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
10160    'OCEANICP', also initialised field pressure correctly in ini_eos in the    'OCEANICP', also initialised field pressure correctly in ini_eos in the
10161    case of pressure coordinates. eosType='JMD95Z' in    case of pressure coordinates. eosType='JMD95Z' in
10162    combination with buoyancyRelation='OCEANICP' now causes an error.    combination with buoyancyRelation='OCEANICP' now causes an error.
10163  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
10164    in find_alpha/beta.    in find_alpha/beta.
10165  checkpoint46d_pre  checkpoint46d_pre (2002/08/15)
10166    
10167  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
10168    so that JMD95Z and JMD95P give approptiate static stability in find_rho.    so that JMD95Z and JMD95P give approptiate static stability in find_rho.
10169    
10170  checkpoint46c_post  checkpoint46c_post (2002/08/15)
10171  o Changes necessary for ocean in p-coordinates  o Changes necessary for ocean in p-coordinates
10172   -  Added new buoyancy relation = 'OCEANICP'   -  Added new buoyancy relation = 'OCEANICP'
10173   -  Added new parameters = gravitySign (this used to be contained inside   -  Added new parameters = gravitySign (this used to be contained inside
10174      the factor dRdZ which I added when we first switched to R coordinates).      the factor dRdZ which I added when we first switched to R coordinates).
10175   X GM/Redi is not compatible (yet)   X GM/Redi is not compatible (yet)
10176   X bottom drag and no-slip need to be debugged.   X bottom drag and no-slip need to be debugged.
10177  checkpoint46c_pre  checkpoint46c_pre (2002/08/07)
10178    
10179  checkpoint46b_post  checkpoint46b_post (2002/08/07)
10180  o Added new equation of state -> JMD95Z and JMD95P  o Added new equation of state -> JMD95Z and JMD95P
10181    - EOS of Jackett and McDougall, 1995, JAOT    - EOS of Jackett and McDougall, 1995, JAOT
10182    - moved all EOS parameters into EOS.h    - moved all EOS parameters into EOS.h
# Line 1592  o Added UNESCO EOS, but not recommended Line 10185  o Added UNESCO EOS, but not recommended
10185    in-situ temperature (see JMD95)    in-situ temperature (see JMD95)
10186  o Modified formatting for knudsen2.f in utils/knudsen2 and added  o Modified formatting for knudsen2.f in utils/knudsen2 and added
10187    unesco.f to be used with POLY3    unesco.f to be used with POLY3
10188  checkpoint46b_pre  checkpoint46b_pre (2002/07/31)
10189    
10190  checkpoint46a_post  checkpoint46a_post (2002/07/31)
10191  o Added (atmospheric) pressure loading  o Added (atmospheric) pressure loading
10192    - new field in FFIELDS.h, etc...    - new field in FFIELDS.h, etc...
10193    - new cpp flag ATMOSPHERIC_LOADING    - new cpp flag ATMOSPHERIC_LOADING
10194  o Changed hFacC to _hFacC in calc_phi_hyd.F  o Changed hFacC to _hFacC in calc_phi_hyd.F
10195  o Added SHORTWAVE_HEATING to some files for consistency  o Added SHORTWAVE_HEATING to some files for consistency
10196  checkpoint46a_pre  checkpoint46a_pre (2002/07/13)
10197    
10198  checkpoint46  checkpoint46 (2002/07/13)
10199  further merges from release1_p5  further merges from release1_p5
10200  o new ctrl package  o new ctrl package
10201    - adopted from ECCO environment to enable optimization    - adopted from ECCO environment to enable optimization
# Line 1629  o added hooks for Eliassen Palm fluxes ( Line 10222  o added hooks for Eliassen Palm fluxes (
10222  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
10223  o incorporated hooks for sponge layer code (external_forcing.F)  o incorporated hooks for sponge layer code (external_forcing.F)
10224    
10225  checkpoint45d_post  checkpoint45d_post (2002/07/12)
10226  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
10227  o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S  o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
10228    (affects plume_on_slope "cg2d" output)    (affects plume_on_slope "cg2d" output)
# Line 1643  o add new flags: Line 10236  o add new flags:
10236   - for each tracer, define internal flag for multiDimAdvection & A-B   - for each tracer, define internal flag for multiDimAdvection & A-B
10237  o monitor: change definition of KE to check conservation of Energy  o monitor: change definition of KE to check conservation of Energy
10238    
10239  checkpoint45c_post  checkpoint45c_post (2002/05/30)
10240  o Removed f90 comments ("!")  o Removed f90 comments ("!")
10241  o Modified initialisations to enable exf package for MITgcm  o Modified initialisations to enable exf package for MITgcm
10242    (without invoking ECCO_PACKAGE).    (without invoking ECCO_PACKAGE).
# Line 1651  o modifications to gradient check packag Line 10244  o modifications to gradient check packag
10244    - enable centered differences    - enable centered differences
10245    - modified format of standard output    - modified format of standard output
10246    
10247  checkpoint45b_post  checkpoint45b_post (2002/05/30)
10248  o cleaned exchange calls in cg2d  o cleaned exchange calls in cg2d
10249  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
10250  o included CPP option SINGLE_LAYER_MODE in thermodynamics  o included CPP option SINGLE_LAYER_MODE in thermodynamics
# Line 1663  o in initialise_varia, moved call packag Line 10256  o in initialise_varia, moved call packag
10256    (corresponding adjustment of TAF tape initialisation).    (corresponding adjustment of TAF tape initialisation).
10257  o in calc_diffusivity/calc_viscosity extended domain to full overlap.  o in calc_diffusivity/calc_viscosity extended domain to full overlap.
10258    
10259  checkpoint45a_post  checkpoint45a_post (2002/05/01)
10260  o compute Rho over the whole domain (extend iMin,jMin indices)  o compute Rho over the whole domain (extend iMin,jMin indices)
10261  o specific exchange for X-slice domain (case Ny=1)  o specific exchange for X-slice domain (case Ny=1)
10262  o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code  o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
# Line 1683  o errorMessageUnit set non-equal zero in Line 10276  o errorMessageUnit set non-equal zero in
10276    (conflict on some platforms, e.g. IBM SP3)    (conflict on some platforms, e.g. IBM SP3)
10277  o modified carbon verif.  o modified carbon verif.
10278    
10279  checkpoint44h_pre  checkpoint44h_pre (2002/03/14)
10280  o vertical grid option: allow to put the Interface at the middle between  o vertical grid option: allow to put the Interface at the middle between
10281    2 cell-centers ; replace delZ in pkg/kpp by drF.    2 cell-centers ; replace delZ in pkg/kpp by drF.
10282  o GM Advective form: Tracers are advected using the residual transport (=  o GM Advective form: Tracers are advected using the residual transport (=
10283    Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.    Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
10284    
10285  checkpoint44g_post  checkpoint44g_post (2002/03/05)
10286  o fix surface correction term in multiDimAdvection (affects plume_on_slope  o fix surface correction term in multiDimAdvection (affects plume_on_slope
10287    results) ; ifdef missing in thermodynamics.F    results) ; ifdef missing in thermodynamics.F
10288    
# Line 1754  o merge of relevant stuff from the ecco- Line 10347  o merge of relevant stuff from the ecco-
10347  o check parameters & config (chkpt44a_pre,post)  o check parameters & config (chkpt44a_pre,post)
10348  o OBC and NonLin_FrSurf.  o OBC and NonLin_FrSurf.
10349    
10350  checkpoint44  checkpoint44 (2002/01/18)
10351  o fix bug in mom_vi_del2uv  o fix bug in mom_vi_del2uv
10352  o select when filters are applied ; add options to zonal_filter (data.zonfilt)  o select when filters are applied ; add options to zonal_filter (data.zonfilt)
10353  o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)  o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
# Line 1762  o update AIM experiments (NCEP input fil Line 10355  o update AIM experiments (NCEP input fil
10355  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
10356  o added some stuff for AD  o added some stuff for AD
10357    
10358  checkpoint43  checkpoint43 (2001/09/28)
10359  o added two new advection tests  o added two new advection tests
10360  o added global 4x4 degree ocean test  o added global 4x4 degree ocean test
10361  o added test of H&S94 with free surface on cube  o added test of H&S94 with free surface on cube
10362  o some final mods for gradient check, adjoint,...  o some final mods for gradient check, adjoint,...
10363    
10364  checkpoint42  checkpoint42 (2001/09/27)
10365    Fixed AD-related problems:    Fixed AD-related problems:
10366  o Store directives up-to-date with re-arranged Adams-Bashforth  o Store directives up-to-date with re-arranged Adams-Bashforth
10367    (mainly thermodynamics.F)    (mainly thermodynamics.F)
# Line 1780  o Modified store directives for split of Line 10373  o Modified store directives for split of
10373    for the case ALLOW_KPP    for the case ALLOW_KPP
10374  o Cleaned argument list for timestep_tracer.F  o Cleaned argument list for timestep_tracer.F
10375    
10376  checkpoint41  checkpoint41 (2001/09/27)
10377  o re-formatted/added comments in prologues of key subroutines  o re-formatted/added comments in prologues of key subroutines
10378    to work with protex    to work with protex
10379    
10380  checkpoint40  checkpoint40 (2001/09/27)
10381  o moved calc_gs, calc_gt and calc_tr1 back to model/src  o moved calc_gs, calc_gt and calc_tr1 back to model/src
10382  o added FLT (floats) package from Arne along with demo. experiment  o added FLT (floats) package from Arne along with demo. experiment
10383  o re-arranged Adams-Bashforth scheme for tracers to allow easier  o re-arranged Adams-Bashforth scheme for tracers to allow easier
# Line 1793  o more mods for non-linear free-surface Line 10386  o more mods for non-linear free-surface
10386  o modified multi-dim method to work on cube  o modified multi-dim method to work on cube
10387  o bug fix in KPP (from DM)  o bug fix in KPP (from DM)
10388    
10389  checkpoint40pre9  checkpoint40pre9 (2001/09/27)
10390  o added DST advection schemes  o added DST advection schemes
10391  o fix MPI bug on SGI's  o fix MPI bug on SGI's
10392  o modifications for non-linear free-surface  o modifications for non-linear free-surface
# Line 1803  o changes to commenting of arguments for Line 10396  o changes to commenting of arguments for
10396  o added/updated many matlab scripts  o added/updated many matlab scripts
10397  o added multi-dimensional advection method for tracers  o added multi-dimensional advection method for tracers
10398        
10399  checkpoint40pre8  checkpoint40pre8 (2001/09/05)
10400  o new package rw/  o new package rw/
10401    Added method for dumping intermediate local arrays:    Added method for dumping intermediate local arrays:
10402    mdsio_writetile - same as mdsio_writefield except works from inside    mdsio_writetile - same as mdsio_writefield except works from inside
# Line 1822  o TAMC-related update to cope with mom_f Line 10415  o TAMC-related update to cope with mom_f
10415    currently nothing implemented to switch this storing off    currently nothing implemented to switch this storing off
10416    in case fluxform is used since no CPP flag available).    in case fluxform is used since no CPP flag available).
10417    
10418  checkpoint40pre7  checkpoint40pre7 (2001/08/14)
10419  o bug fix in dynamics.F  o bug fix in dynamics.F
10420    calc_viscosity called before k=1,Nr loop.    calc_viscosity called before k=1,Nr loop.
10421  o added some #ifdef's ALLOW_PASSIVE_TRACER  o added some #ifdef's ALLOW_PASSIVE_TRACER
10422  o cleaned initialisations in ctrl_map_ini  o cleaned initialisations in ctrl_map_ini
10423    related to TAF    related to TAF
10424    
10425  checkpoint40pre6  checkpoint40pre6 (2001/08/13)
10426  o split dynamics into thermodynamics & dynamics  o split dynamics into thermodynamics & dynamics
10427  o corresponding split of calc_diffusivity into  o corresponding split of calc_diffusivity into
10428    calc_diffusivity, calc_viscosity    calc_diffusivity, calc_viscosity
# Line 1837  o corresponding split of calc_diffusivit Line 10430  o corresponding split of calc_diffusivit
10430  o Added diffkr, kapgm to control variables  o Added diffkr, kapgm to control variables
10431  o bug fix in gmredi_slope_limit for ldd97  o bug fix in gmredi_slope_limit for ldd97
10432    
10433  checkpoint40pre5  checkpoint40pre5 (2001/07/31)
10434  o proper initialization of Adams-Bashforth time stepping  o proper initialization of Adams-Bashforth time stepping
10435    + uses forward step for very first step of model (iter=0)    + uses forward step for very first step of model (iter=0)
10436  o re-generated *all* output since almost all output is modified by this  o re-generated *all* output since almost all output is modified by this
# Line 1851  o added new expt "solid-body.cs-32x32x1" Line 10444  o added new expt "solid-body.cs-32x32x1"
10444    + this uses an alternative form of ini_curvilinear_grid.F which    + this uses an alternative form of ini_curvilinear_grid.F which
10445      is not necessarily any better than the current one...      is not necessarily any better than the current one...
10446    
10447  checkpoint40pre4  checkpoint40pre4 (2001/07/30)
10448  o added re-initialisations of utrans,vtrans,rtrans in  o added re-initialisations of utrans,vtrans,rtrans in
10449    calc_common_factors which are crucial for TAF.    calc_common_factors which are crucial for TAF.
10450  o extended iMin,jMin range for calc_common_factors,  o extended iMin,jMin range for calc_common_factors,
# Line 1859  o extended iMin,jMin range for calc_comm Line 10452  o extended iMin,jMin range for calc_comm
10452  o added option ALLOW_PASSIVE_TRACER  o added option ALLOW_PASSIVE_TRACER
10453  o a few minor updates and fixes  o a few minor updates and fixes
10454    
10455  checkpoint40pre3  checkpoint40pre3 (2001/07/13)
10456  o created calc_gtr1.F for gad package  o created calc_gtr1.F for gad package
10457  o split the_main_loop and re-introduced forward_step  o split the_main_loop and re-introduced forward_step
10458  o some recomputations of nIter0 for TAMC  o some recomputations of nIter0 for TAMC
10459    
10460  checkpoint40pre2  checkpoint40pre2 (2001/07/13)
10461  o Updated to latest branch of AJA, JMC  o Updated to latest branch of AJA, JMC
10462  o Added gradient check package  o Added gradient check package
10463  o Added routines for passive tracer handling  o Added routines for passive tracer handling
10464  o Added carbon sequestration sensitivity experiment  o Added carbon sequestration sensitivity experiment
10465    
10466  checkpoint39  checkpoint39 (2001/05/14)
10467   o Modifications and fixes to support TAMC   o Modifications and fixes to support TAMC
10468     (mainly missing or wrong directives)     (mainly missing or wrong directives)
10469   o Corrected common blocks when fooling TAMC to produce adjoint I/O   o Corrected common blocks when fooling TAMC to produce adjoint I/O
# Line 1884  checkpoint39 Line 10477  checkpoint39
10477           (NB: this is not the full ECCO environment)           (NB: this is not the full ECCO environment)
10478   o disabled some packages by default in genmake   o disabled some packages by default in genmake
10479    
10480  checkpoint38  checkpoint38 (2001/04/10)
10481   o see notes_c37_adj.txt   o see notes_c37_adj.txt
10482   o corrected wrong layer index in external_forcing_t   o corrected wrong layer index in external_forcing_t
10483   o replaced the_main_loop/forward_step by the_main_loop   o replaced the_main_loop/forward_step by the_main_loop
# Line 1892  checkpoint38 Line 10485  checkpoint38
10485     (replaced criteria for initial/final state)     (replaced criteria for initial/final state)
10486   o added runtime flag for pre-C35 pickups: usePickupBeforeC35   o added runtime flag for pre-C35 pickups: usePickupBeforeC35
10487    
10488  checkpoint37  checkpoint37 (2001/03/13)
10489   o mdsio.F routine split and packaged in pkg/mdsio   o mdsio.F routine split and packaged in pkg/mdsio
10490     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
10491      used unless genmake -disable=mdsio)      used unless genmake -disable=mdsio)
# Line 1909  checkpoint37 Line 10502  checkpoint37
10502   o Non-Hydrostatic pickup file Pb fixed.   o Non-Hydrostatic pickup file Pb fixed.
10503   o bug with Rigid-lid version (since c35) fixed.     o bug with Rigid-lid version (since c35) fixed.  
10504    
10505  checkpoint36  checkpoint36 (2001/02/20)
10506   o implement Crank-Nickelson barotropic time-stepping   o implement Crank-Nickelson barotropic time-stepping
10507   o recover Time-Average diagnostics   o recover Time-Average diagnostics
10508   o fix Pb in checkpoint (PR#19)   o fix Pb in checkpoint (PR#19)
10509   o AIM become a standard package ; clean unused CPP_kees   o AIM become a standard package ; clean unused CPP_kees
10510    
10511  checkpoint35  checkpoint35 (2001/02/08)
10512   o subtantial rewrite of dynamics.f   o subtantial rewrite of dynamics.f
10513   o allows staggered time-stepping   o allows staggered time-stepping
10514   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
10515   o added bottom drag (linear + quadratic)   o added bottom drag (linear + quadratic)
10516    
10517  checkpoint34  checkpoint34 (2001/01/30)
10518   o Modified exchange routines for correct reverse simulation.   o Modified exchange routines for correct reverse simulation.
10519   o Added verification output to comply with bug fix in impldiff.F   o Added verification output to comply with bug fix in impldiff.F
10520     as of c33 (exp2, natl_box).     as of c33 (exp2, natl_box).
# Line 1932  checkpoint34 Line 10525  checkpoint34
10525   o Added routine GLOBAL_SUM_INT to global_sum.F   o Added routine GLOBAL_SUM_INT to global_sum.F
10526   o Added mdsio_gl.F for ECCO purposes.   o Added mdsio_gl.F for ECCO purposes.
10527    
10528  checkpoint33  checkpoint33 (2000/11/30)
10529   o Fixed bug in lower BC in impldiff.F   o Fixed bug in lower BC in impldiff.F
10530   o Fixed confusion about units of forcing arrays in FFIELDS.h   o Fixed confusion about units of forcing arrays in FFIELDS.h
10531     namely Fu,Fv,Qnet,Qsw,EmPmR:     namely Fu,Fv,Qnet,Qsw,EmPmR:
# Line 1950  checkpoint33 Line 10543  checkpoint33
10543       possibly use them.       possibly use them.
10544   o Corrected genmake to delete a temporary file during configuration   o Corrected genmake to delete a temporary file during configuration
10545    
10546  checkpoint32  checkpoint32 (2000/11/13)
10547   o Scaling of forcing fields moved from external_forcing.F to   o Scaling of forcing fields moved from external_forcing.F to
10548     external_fields_scale.F, called directly after loading fields.     external_fields_scale.F, called directly after loading fields.
10549   o Surface relaxation terms added to surface tendency fields in   o Surface relaxation terms added to surface tendency fields in
# Line 1961  checkpoint32 Line 10554  checkpoint32
10554   o Modifications and bug fixes in KPP package.   o Modifications and bug fixes in KPP package.
10555   o Verification experiment for KPP added (verification/nat_box/)   o Verification experiment for KPP added (verification/nat_box/)
10556    
10557  checkpoint31  checkpoint31 (2000/09/11)
10558   o Packages interface brought in line with defined standard   o Packages interface brought in line with defined standard
10559     -> new routines packages_...F     -> new routines packages_...F
10560     -> changes in initialise_fixed.F, initialise_varia.F     -> changes in initialise_fixed.F, initialise_varia.F
# Line 1978  checkpoint31 Line 10571  checkpoint31
10571     - not yet tested for GMRedi.     - not yet tested for GMRedi.
10572     - not yet tested for KPP.     - not yet tested for KPP.
10573    
10574  checkpoint30  checkpoint30 (2000/07/13)
10575   o Updates for OBCs   o Updates for OBCs
10576   o New experiment for test OBCs (internal_wave)   o New experiment for test OBCs (internal_wave)
10577   o New output.txt in verification/exp4/results/   o New output.txt in verification/exp4/results/
# Line 1987  checkpoint30 Line 10580  checkpoint30
10580   o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)   o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
10581     and entry for T90 in genmake     and entry for T90 in genmake
10582    
10583  checkpoint29  checkpoint29 (2000/06/21)
10584   o packaged KPP and GM/Redi   o packaged KPP and GM/Redi
10585    
10586  checkpoint28  checkpoint28 (2000/06/09)
10587   o Corrected initialization of hFacMin for difference vertical coordinates   o Corrected initialization of hFacMin for difference vertical coordinates
10588   o Modified calculation of partial cell thickness to more robust algorithm   o Modified calculation of partial cell thickness to more robust algorithm
10589   o config_summary.F: replaced write_1D_... by write_0D_...   o config_summary.F: replaced write_1D_... by write_0D_...
# Line 2003  checkpoint28 Line 10596  checkpoint28
10596     included store directives and tape key computations required for TAMC.     included store directives and tape key computations required for TAMC.
10597   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
10598    
10599  checkpoint27  checkpoint27 (2000/04/10)
10600   o fixed calc_isoslopes() to so that cancellation of terms in tensor   o fixed calc_isoslopes() to so that cancellation of terms in tensor
10601     formulation works properly with variable resolution.     formulation works properly with variable resolution.
10602   o restructured the calling tree between the_model_main() and dynamics()   o restructured the calling tree between the_model_main() and dynamics()
# Line 2011  checkpoint27 Line 10604  checkpoint27
10604   o introduced initialization file pSurfInitFile for free surface (cg2d_x)   o introduced initialization file pSurfInitFile for free surface (cg2d_x)
10605     in new routine ini_psurf()     in new routine ini_psurf()
10606    
10607  checkpoint26  checkpoint26 (2000/04/05)
10608   o moved some #ifdef in optional routines to encompass everything   o moved some #ifdef in optional routines to encompass everything
10609     except the argument declarations. This was using up some memory.     except the argument declarations. This was using up some memory.
10610   o fixed macros like _ADT to work with both versions of Linux cpp   o fixed macros like _ADT to work with both versions of Linux cpp
# Line 2021  checkpoint26 Line 10614  checkpoint26
10614     (macros are now in eesupp/inc/CPP_EEMACROS.h)     (macros are now in eesupp/inc/CPP_EEMACROS.h)
10615   o patch for 2 processor JAM mode   o patch for 2 processor JAM mode
10616    
10617  checkpoint25  checkpoint25 (2000/03/15)
10618   o updates for OBCs and NH   o updates for OBCs and NH
10619   o dramatically reduced memory usage   o dramatically reduced memory usage
10620   o added "JAM" routines for use on Artic network   o added "JAM" routines for use on Artic network
# Line 2032  checkpoint25 Line 10625  checkpoint25
10625      an explicit free-surface option)      an explicit free-surface option)
10626   o initial state input files for U and V   o initial state input files for U and V
10627    
10628  checkpoint24  checkpoint24 (1999/08/02)
10629   o Removed some spurious "REAL"s   o Removed some spurious "REAL"s
10630   o Updated KPP to latest version from JPL   o Updated KPP to latest version from JPL
10631   o Added a COS(latitude) in horizontal viscosity   o Added a COS(latitude) in horizontal viscosity
10632    
10633  checkpoint23  checkpoint23 (1999/05/26)
10634   o Added del^4 diffusion for salt and temperature   o Added del^4 diffusion for salt and temperature
10635   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
10636    
10637  checkpoint22  checkpoint22 (1999/05/18)
10638   o Made many small changes: implicit none, format(i5), etc...   o Made many small changes: implicit none, format(i5), etc...
10639   o Introduced KPP mixing scheme (compiles and runs but *not* tested)   o Introduced KPP mixing scheme (compiles and runs but *not* tested)
10640    
10641  checkpoint21  checkpoint21 (1999/05/18)
10642   o Introduced new I/O package that supports direct-access records (mdsio.F)   o Introduced new I/O package that supports direct-access records (mdsio.F)
10643   o Split-up mid-level I/O routines   o Split-up mid-level I/O routines
10644   o Updated input data for experiments 0,1,2,4 and 5   o Updated input data for experiments 0,1,2,4 and 5
10645   o Finally removed the genmake.* scripts (everyone seems happy with genmake)   o Finally removed the genmake.* scripts (everyone seems happy with genmake)
10646    
10647  checkpoint20  checkpoint20 (1999/03/22)
10648   o Tidied up open-boundaries some more   o Tidied up open-boundaries some more
10649   o Added non-hydrostatic code   o Added non-hydrostatic code
10650   o Fixed some input data   o Fixed some input data
10651   o Modified MPI start-up to work in "coupled" context.   o Modified MPI start-up to work in "coupled" context.
10652    
10653  checkpoint19  checkpoint19 (1998/12/15)
10654   o Tidied up directory structure for verification experiments.   o Tidied up directory structure for verification experiments.
10655   o Added new code for open boundaries.   o Added new code for open boundaries.
10656   o Corrected advective terms near boundaries.   o Corrected advective terms near boundaries.
# Line 2065  checkpoint19 Line 10658  checkpoint19
10658   o Implemented free-slip/no-slip BCs and del^4 dissipation.   o Implemented free-slip/no-slip BCs and del^4 dissipation.
10659   o Split default parameters out of ini_parms.F into set_defaults.F.   o Split default parameters out of ini_parms.F into set_defaults.F.
10660    
10661  checkpoint18  checkpoint18 (1998/11/30)
10662   o Further changes for optional code generation with   o Further changes for optional code generation with
10663     CPP - ugh!     CPP - ugh!
10664    
10665  checkpoint17  checkpoint17 (1998/11/03)
10666   o Beginning to incorporating modularity   o Beginning to incorporating modularity
10667     for supporting atmos. and ocean configs.     for supporting atmos. and ocean configs.
10668   o Small changes for TAMC complinace   o Small changes for TAMC complinace
10669   o New ultra simple test case. Barotropic box   o New ultra simple test case. Barotropic box
10670     configuration "exp0".     configuration "exp0".
10671    
10672  checkpoint16  checkpoint16 (1998/10/28)
10673   o Minor changes to exchange routines to support   o Minor changes to exchange routines to support
10674     accumulation in reverse mode. Adjoint of an     accumulation in reverse mode. Adjoint of an
10675     assignment is an addition.     assignment is an addition.
# Line 2084  checkpoint16 Line 10677  checkpoint16
10677     syntax) and by g77 under Linux ( 72 character     syntax) and by g77 under Linux ( 72 character
10678     limit ).     limit ).
10679    
10680  checkpoint15  checkpoint15 (1998/09/29)
10681   Rewrote exchange routines to allow   Rewrote exchange routines to allow
10682   o General tile <-> tile connectivity.   o General tile <-> tile connectivity.
10683   o TAMC reverse mode flag ( is this really needed? )   o TAMC reverse mode flag ( is this really needed? )
# Line 2093  checkpoint15 Line 10686  checkpoint15
10686     shmput/shmget, VIA, SYSV shmem and every other cool     shmput/shmget, VIA, SYSV shmem and every other cool
10687     communication method.     communication method.
10688    
10689  checkpoint14  checkpoint14 (1998/09/09)
10690   Consistent isomorphism chages made. These allow dynamical core   Consistent isomorphism chages made. These allow dynamical core
10691   to support both pressure and meters as a vertical coordinate.   to support both pressure and meters as a vertical coordinate.
10692    
10693  checkpoint13  checkpoint13 (1998/07/17)
10694   Release which corrects global_max problem and a couple   Release which corrects global_max problem and a couple
10695   of KGM time-averaging diagnostic errors. Also contains   of KGM time-averaging diagnostic errors. Also contains
10696   a double-gyre experiment setup as well as the baseline   a double-gyre experiment setup as well as the baseline
# Line 2112  branch-point-rdot Line 10705  branch-point-rdot
10705   I don't want to commit the rDot to the main-trunk until   I don't want to commit the rDot to the main-trunk until
10706   we've actually tested it...   we've actually tested it...
10707    
10708  checkpoint12  checkpoint12 (1998/07/08)
10709   Tidy up and added generic genmake script (formerly   Tidy up and added generic genmake script (formerly
10710   configure script).   configure script).
10711   Released to testers.   Released to testers.
10712    
10713  checkpoint11  checkpoint11 (1998/07/02)
10714   Re-arranged initialise() and introduced ini_vertical_grid()   Re-arranged initialise() and introduced ini_vertical_grid()
10715   and ini_masks_etc().   and ini_masks_etc().
10716    
10717  checkpoint10  checkpoint10 (1998/07/01)
10718   Introduced the configure script.   Introduced the configure script.
10719   Separated out the diags package.   Separated out the diags package.
10720   Added template for writing time-averages of tile/intermediate quantities.   Added template for writing time-averages of tile/intermediate quantities.
10721   Updated SIZE.h in exp2 and made the data big-endian.   Updated SIZE.h in exp2 and made the data big-endian.
10722    
10723  checkpoint9  checkpoint9 (1998/06/22)
10724   MPI fix. Filename changes (meta/data). salbin*y stuff.   MPI fix. Filename changes (meta/data). salbin*y stuff.
10725   General tidy-up.   General tidy-up.
10726   SST.bin SSS.bin added to verification/exp2   SST.bin SSS.bin added to verification/exp2
10727    
10728  checkpoint8  checkpoint8 (1998/06/22)
10729   Inludes time-dependant forcing and time-averaging.   Inludes time-dependant forcing and time-averaging.
10730   Works at 4x4 and 2.8125x2.8125 global   Works at 4x4 and 2.8125x2.8125 global
10731    
# Line 2142  checkpoint7-4degree-ref Line 10735  checkpoint7-4degree-ref
10735   model etc..   model etc..
10736   Configured for verification/exp2 - 4 degree global, two process.   Configured for verification/exp2 - 4 degree global, two process.
10737    
10738  checkpoint7  checkpoint7 (1998/06/15)
10739   Created by cnh   Created by cnh
10740   Simple 4 degree global simulation   Simple 4 degree global simulation
10741   configuration.   configuration.
# Line 2150  checkpoint7 Line 10743  checkpoint7
10743   hydrography, bathymetry etc   hydrography, bathymetry etc
10744   Does not include Heat Flux and E-P   Does not include Heat Flux and E-P
10745    
10746  checkpoint6  checkpoint6 (1998/06/08)
10747   Created by cnh   Created by cnh
10748   merged checkpoint5 with CD and   merged checkpoint5 with CD and
10749   spherical polar code.   spherical polar code.
10750   Still some problems with GM Redi   Still some problems with GM Redi
10751   abd full topography.   abd full topography.
10752    
10753  checkpoint5  checkpoint5 (1998/06/08)
10754   Created by AJA   Created by AJA
10755   contains updates to GM Redi   contains updates to GM Redi
10756   and reordered timestepping loop   and reordered timestepping loop
10757   for Implicit Diffusion.   for Implicit Diffusion.
10758    
10759  checkpoint4  checkpoint4 (1998/05/30)
10760   Created by cnh   Created by cnh
10761   Contains memory saving macros ( _rdxc etc..) for when   Contains memory saving macros ( _rdxc etc..) for when
10762   grid variations are limited.   grid variations are limited.
10763   Contains polynomial coeffs for EOS and knudsen program   Contains polynomial coeffs for EOS and knudsen program
10764   for generation.   for generation.
10765    
10766  checkpoint3  checkpoint3 (1998/05/26)
10767   Created by cnh   Created by cnh
10768   Added extra flags for runtime options   Added extra flags for runtime options
10769   Added this file   Added this file

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