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revision 1.41 by heimbach, Fri Jul 13 18:08:14 2001 UTC revision 1.575 by jmc, Mon Oct 24 18:20:11 2005 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 write grid-file(s) in only one format (MDS or MNC): default=MNC (if
8      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
9    o tracer advection scheme:
10      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
11       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
12       was not very convenient).
13      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
14       (further tests needed for the implicit DST & Flux-Limiter schemes).
15    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
16      and sRef for convenience, handy, when you want to initialize
17      ptracers in a large domain with a constant non-zero value. Also,
18      untangle ptracers_init.F a little.
19    
20    checkpoint57v_post
21    o change dome exp. to use variable viscosity in side-drag terms.
22    o remove all the files from the cfc_offline test since they are now
23      incorporated into tutorial_cfc_offline which has been producing
24      identical results for a few days of testing
25    o add new parameter: sideDragFactor to enable half-slip-side BC
26      and change side-drag S/R to use viscosity from mom_calc_visc
27      (can switch back by setting sideDragFactor=0.); affects results at
28      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
29       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
30    o vorticity & strain are now computed without masking, to account for
31      no-slip-side BC in variable viscosity calculation ; mask is applied
32      anyway later on, before computing advection/coriolis terms.
33    o modify exp4 to test new obcs support for reading from external files
34      and for passive tracers
35    o fix behavior of ptracers_monitor when monitor output is written to a
36      netcdf-file; still not independent of monitor.F (writes in the same
37      file).
38    o change default value of tRef (put a uniform, meaningful value for ocean
39      & atmos) and initialize sRef (was missing, as Martin mentioned).
40    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
41      to be proportional to enstrophy dissipation length.  Thus,
42       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
43      This is now consistent with Smagorinsky and with the manual.
44    
45    checkpoint57u_post
46    o OBCS and PTRACERS: add open boundary support for passive tracers
47      - either use homogenous (pseudo) v.Neumann conditions or prescribe
48        OB-values from file; this is not different from the way theta and salinity
49        are treated
50      - however, Orlanski-radiation conditions are not supported, and the model
51        will stop if you use pTracers and Orlanski at the same time.
52      - beefed up the rountine obcs_external_fields_load: now only those open
53        boundary values are overwritten with values from files for which there
54        are really files, otherwise the OB-fields remain untouched. This makes
55        it possible to use different OBs at different ends of the domain (as
56        with EXF)
57    o reduce number of exch calls in shap_filt (s2).
58    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
59      truncation level) 4/5 MLAdjust test results (11&12 digits match).
60    
61    checkpoint57t_post
62    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
63    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
64      same truncation, independent of the face number: affects affects several
65      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
66    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
67      note that biharmonic viscosity + no-slip was not tested in any experiment.
68    o fix bug in non-linear free-surf side-drag ; generate new output for
69      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
70    o make mnc honor the writeBinaryPrec flag for most kinds of output
71    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
72    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
73      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
74    o add brackets in multi-terms sum to get same truncation, independent of
75      the face number (manage to get exactly same value of gU,gV at the cs-edge)
76      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
77    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
78      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
79      a maximum grid-scale Reynolds number.  Also, changes all length calculations
80      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
81      Suggested values of viscosity parameters found in mom_calc_visc.
82      Many new viscosity diagnostics available.
83    
84    checkpoint57s_post
85    o Add clearing-house for viscosity calculations, mom_calc_visc and
86      correct numerous bugs in LeithD and Smagorinsky discretizations.  
87      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
88      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
89      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
90      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
91      The Strain-Tension form is now called with useStrainTensonVisc=.true.
92      ViscAhStrain and viscAhTension are now retired.
93    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
94    o In response to JMC's bug report, genmake2 now ignores any soft-links
95      that it finds in the *current* directory when searching for files.
96      Soft-links found in any other source directories will still work as
97      they did before.
98    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
99      a C routine to unlimit the stack size
100    o mnc-ify pkg/aim snapshot vars
101    o mnc-ify pkg/land as requested by Daniel
102    o various changes to mnc including:
103      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
104      - output can now be grouped so that all files within a group
105          change the ITER portion of their names in lock-step together
106      - can now read ("global") PER-FACE (in addition to PER-TILE) files
107          and works with both EXCH1 and EXCH2 (but needs more testing)
108      - writing works for all verification test cases w/ g77 on Linux
109    
110    checkpoint57r_post
111    o make MNC variable initialization happen earlier
112    o add diagnostics for (almost) each term of the momentum Eq.
113    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
114    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
115    o remove MINIMAL_TAVE_OUTPUT option ;
116      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
117    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
118      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
119    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
120    o add time-dependent SST, SSS control
121    o cost terms in ecco/ modularized (new cost_generic.F)
122    o cost_averages routines are modularized (new cost_averagesgeneric.F)
123    o new infrastructure for seaice model vs. obs misfits in seaice/
124      * driver from the_main_loop.F is seaice_cost_driver.F
125      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
126      * gradient check in Exp. 6a of natl_box_adjoint/
127    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
128      (see README file)
129    
130    checkpoint57q_post
131    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
132    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
133      - bug was reported by Jean-Michel and Ian Fenty
134    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
135      update exp. cpl_aim+ocn output.
136    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
137      Needed for high-res. runs with large global files
138      to be able to limit tapelev size
139    o Changed some tests for adjoint:
140      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
141      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
142      * global_ocean.90x40x15/ back to default 3-level checkpointing
143    o Modifications to enable scripted COMMON to MODULE conversion
144      * verification/OpenAD/code/ has necessary scripts and description;
145      * converts, compiles and runs successfully;
146    
147    checkpoint57p_post
148    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
149    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
150      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
151    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
152    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
153      (was already the case for dissipation with mom_vecinv,
154       and also the case for grad.PhiHyd when staggered-timeStep)
155      This will allow to put dissipation out-off the AB time-stepping.
156     Unfortunately, affects truncation error. Update output of exp. that "fails"
157      (cg2d matching number) and leave the others for later: front_relax(10),
158      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
159      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
160    
161    checkpoint57o_post
162    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
163      (2) its ready to be documented during the 20050801 DocFest
164    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
165      for ideal_2D_oce and lab_sea on linux_ia32_g77
166    o set to #undef CTRL_SET_OLD_MAXCVARS_30
167      in global1x1_tot/code_seaice_adj to access indices 32, 33
168      (worth another tag)
169    
170    checkpoint57n_post
171    o adding precip control xx_precip 32
172    o adding swflux control xx_swflux 33
173    o Replacing 10 forcing penalty cost routines by 1 generic.
174    o Implementing partitioning in time-mean and variable adjustment
175      for atmos. state.
176    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
177    o in natl_box_adjoint:
178      * updated exp 1 to 10
179        (but does not have time-mean vs. variable split results yet)
180    o updated global1x1/*_seaice_adj/
181      to incorporate latest changes
182    o enable useSingleCpuIO for mdsio vector routines
183      (applies in particular to tapelev I/O)
184    o removed inefficient K-loop in all active_file*control*.F
185    
186    checkpoint57m_post
187    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
188      and advect_cs (use EXCH-2 and standard cs-32 grid files).
189    o pkg/exch2: filling of face-corner halo regions is optional
190      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
191    
192    checkpoint57l_post
193     tag before updating tutorials (pre-release-2)
194    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
195       for output and interpolation of input fields onto model grid)
196    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
197       Affects results of exp. rotating_tank ; update output.txt.
198    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
199          and taking the square quantity and/or using a fraction-weight field.
200    o fix aim_diagnostics_init.F mate numbers.
201    o add mnc output capability to diagnostics/diagstat and update
202      our cvsignore files for the ACSII output generated
203    
204    checkpoint57k_post
205    o lab_sea now uses diagnostics package and provides a suite of
206      new EXF diagnostics output.
207    
208    checkpoint57j_post
209    o exf
210      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
211        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
212        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
213      * extended diagnostics output
214        - now includes all EXF variables
215        - hs, hl moved to common block
216        - separate S/R for diagnostics, called after ctrl vector is added
217        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
218        - EXFqnet contains true Qnet (i.e. includes qsw)
219      * updated verif. lab_sea, global_with_exf
220      * Rearranging hflux (exf_mapfields -> exf_getforcing)
221        to ensure that diagnostics sees a true EXFqnet
222    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
223    o diagnostics pkg: change pointers so that 1 diagnostic can be used
224      several times with different frequencies.
225    o mnc-ify the thsice package as requested by Daniel Enderton
226      - the monitor--MNC output needs work
227      - many attributes need to be added (most are currently blank)
228    o mnc-ify theaim_v23 package as requested by Daniel Enderton
229      - many attributes need to be added (most are currently blank)
230    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
231    o add Sadourny like discretization to the 4th.O vorticity advection scheme
232    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
233      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
234         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
235    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
236     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
237    
238    checkpoint57i_post
239    o Diagnostics package was changed: diagnostic allocation is now deactivated
240      by setting an empty file name in the namelist (used to be by setting 0 frequency)
241    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
242      add 1rst Order upwind vertical Shear.
243    o add a quick fix for A/B checkpointing in OFFLINE mode
244    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
245      end-run around the C/Fortran linking horror in eesup/src/timers.F
246    o added pkg/runclock: allows user to terminate run based on wall clock
247    o added non-hydrostatic scaling parameter: nh_am2
248    o pkg/my82: futile attempt to make results compiler-independent by adding
249      some "_d 0", etc. no effect.
250    o for mnc output, fill the 'T' coordinate var with myTime and create a
251      separate 'iter' variable for iteration count
252    o pkg/diagnostics:
253      add new capability: output of Global/Regional & per-level statistics ;
254      tested against monitor output (including land & thSIce) on various exp.
255    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
256    
257    checkpoint57h_done
258      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
259      data.diagnostics, data.gchem, data.ptracers) is done.
260    
261    o pkg/diagnostics: prepare for Global/Regional statistics.
262      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
263    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
264      and rename it: DIFFERENT_MULTIPLE
265    
266    checkpoint57h_post
267    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
268    o pkg/diagnostics: change output frequency, now in seconds (instead
269      of Nb of iterations). This requires to change data.diagnostics.
270    checkpoint57h_pre
271    
272    o in mnc, let the user create the output dir if both mnc_outdir_date
273      and mnc_outdir_num are false
274    o add fflags() to pkg/diagnostics which allows one to specify, on a
275      per-file basis, the file precision [default behavior is unchanged]
276    o added diagnostics to pkg/kpp, including computation of mixed layer
277      depth based on a temperature/density criterion
278    o updated verification/natl_box to test the new pkg/kpp diagnostics
279    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
280    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
281    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
282      not mnc -- this mistake was found by JMC and is now corrected
283    
284    checkpoint57g_post
285    o add Adams-Bashforth 3rd Order time stepping:
286      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
287      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
288    checkpoint57g_pre
289    
290    o make lambda[Theta,Salt]ClimRelax spatially varying
291      (default remains spatially uniform constant based on tau)
292    o added new control variables
293      * init. uVel, vVel, etanN
294      * lambda[Theta,Salt]ClimRelax
295    o separate masks used for ctrl_pack/unpack 'from write_grid' output
296      (suggested by G. Forget)
297    
298    checkpoint57f_post
299    o add parameter "baseTime" = model base time = time at iteration zero
300      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
301      account for baseTime shift
302    o move Coriolis arrays from PARAMS.h to GRID.h
303    checkpoint57f_pre
304    
305    o mnc-ifying the seaice package
306    o introduced an alternative length scale calculation for use in the limiting
307      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
308    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
309    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
310      as well as grad(vort3).  Made it compatible with both approximate form
311      for the cubed sphere and full form of these gradients.  Added flag
312      useFullLeith to select between approximate and full form.  
313    o add "d0" in getcon.F to reduce differences between compilers/platforms
314      update output.txt of exp. fizhi-gridalt-hs
315    o change port_rand funtion to allow to set the seed.
316    o fix obscure MNC bug involving conversion between reals and integers
317      - it caused no problems with certain (eg. gcc, ifc) compilers but the
318        new version is now more standards-compliant
319    o adjoint-related modifications
320      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
321      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
322      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
323    
324    checkpoint57e_post
325    o Adding eddy stress controls a la Ferreira et al.
326    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
327    
328    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
329      update output.txt of exp. fizhi-gridalt-hs
330    o add more "Z" dimensions and associated coordinate vars to MNC
331    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
332    o parameter calendarDumps: when set, approximate months (30-31 days) and years
333      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
334      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
335      months and years.  Requires pkg/cal.
336    o diagnostics: add pickup functionality
337      - off by default for backwards compatibility
338      - current version only uses MDSIO -- MNC will be added
339    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
340    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
341    
342    checkpoint57d_post
343    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
344    o modify verification/ideal_2D_oce so that it tests the creation of mnc
345      output from the diagnostics package
346    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
347    o make genmake2 more portable by using ".$FS" instead of ".f" for more
348      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
349    o add coordinate variables to the MNC output from the diagnostics package
350    o change MNC-flags default value: true when useMNC=TRUE
351    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
352      the ability (off by default) to read the grid information using MNC
353    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
354    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
355    o do snap-shot diagnostics at the middle of the time-interval (instead of
356      at the end).
357    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
358      new test for AIM with thSIce + slab-ocean
359    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
360    o move state variable diagnostics to the beginning of the time step ;
361      (note: still needs some work specially for snap-shot diagnostics)
362      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
363    
364    checkpoint57c_post
365    o Change testing option (-ieee) to get closer agreement between g77 & ifort
366    o generate new output.txt files on faulks with g77 & the new -ieee option
367    checkpoint57c_pre
368    
369    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
370      update output.txt of exp. global_ocean.90x40x15
371    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
372      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
373    o add saltFlux(+File) forcing capability with periodicExternalForcing
374    o allow to use pkg diagnostics for GM-Redi & ThSIce output
375    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
376    o improvements for the MNC output from DIAGNOSTICS:
377      - correct handling of the unlimitied dimension
378      - all dims now have associated coordinate variables
379      - variables located at U, V, and Corner ("Z") points are now written
380        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
381        *all* data points are output
382    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
383    o added pkg/seaice/seaice_monitor.F
384    o mdsio_readfield.F can now read files visible only to master MPI process.
385    o pkg/seaice: some test code for ice-modified ocean stress
386    o exf_getffields interpolation defaults to bilinear for all scalar forcing
387      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
388      spurious negative numbers for precipitation and humidity.  Will cause
389      some small numerical differences for integrations using pkg/exf/exf_interp.F.
390    o pkg/ctrl/
391      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
392        May be enabled via doPackDiag
393      *  introduce z-scaling of
394         + gradient (doZscalePack) and
395         + control (doZscaleUnpack)
396    o pkg/mdsio/
397      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
398      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
399    
400    checkpoint57b_post
401    o simplify options in diagnostics_fill arguments (remove weird combinations)
402    o fix MNC coordinate variables so that they now contain per-face index
403      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
404      general, EXCH2 grids are only aligned to a "local" coordinate system
405    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
406    o Implement instantaneous output within pkg diagnostics:
407      setting a negative frequency in data.diagnostics produces
408     "snap-shot" output (as opposed to time-average if freq > 0)
409    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
410      NOTE: change ptracer diagnostics name: use 2 characters to work with
411            more than 9 tracers. Add also diagnostics of advect & diffus flux.
412    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
413      becomes the coordinate variable for the 'T' dimension
414    o add CF-style coordinate variables to MNC
415      - just a first cut:  numbers are meaningless on the cubesphere and
416        missing along the T axis but otherwise it works!
417    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
418    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
419    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
420      this is based directly on what the model compute, so that the content of
421      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
422    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
423    o clean up build options files for SunOS, in particular
424      - remove -traditional from xmakedepend
425      - change -xarch=v9 to -xarch=native for f77
426      - restore use of make (not gmake)
427      - add CC=gcc if using g77
428    o changes per discussion of AM, JMC, & EH3 today:
429      - move redundant "grid" variables out of "state" -- in preparation of
430        creating proper CF-style coordinate variables and in recognition
431        that any/all grid variables can be easily copied (eg. w/NCO) from
432        the grid files into any of the other NetCDF files
433      - *always* output grid variables with MDSIO (this will eventually be
434        changed)
435      - output MNC grid file if useMNC is true
436    o every instance of _END_MASTER() has been found and replaced with
437      _END_MASTER( myThid ) in order to satisfy certain picky Sun
438      preprocessors
439    o re-arrange diagnostics pkg initialisation:
440     - allow each package to extend the available diagnostics list
441     - add some checking and fix small problems (multi-threaded, ...)
442     - new S/R diagnostics_fill (replace fill_diagnostics):
443       look through the short list of active diag. (instead of the long list)
444       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
445    
446    checkpoint57a_post
447    o this set of changes restores TAMC compatibility
448      tested for global_ocean.90x40x15 adjoint on trough
449      (what a pain)
450    
451    checkpoint57a_pre
452    o some modifs in tools/build_options for sunos
453    o call ctrl_pack for ctrl at end for optimcycle=0
454    
455    checkpoint57
456    o add horizontal bi-harmonic viscosity for vertical velocity
457      - new parameter viscA4W (defaults to viscA4)
458      - affects only non-hydrostatic code
459      - to be done: no-slip lateral boundary conditions
460    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
461    o implement Implicit Vertical advection for pTracers
462    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
463      (implemented also for implicit vertical diffusion & advection)
464    o OBCS: extend application of tracer open boundary conditions
465      to a strip beyond the boundary of width Olx/Oly
466    o add call monitor to TAF set of required calls (flow directives)
467      and include in natl_box_adjoint
468    o untangle a few ifdefs related to cost, ctrl, autodiff
469      untangel a few ALLOW_ECCO_OPTIMIZATION
470    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
471      (theta2, salt2 in ecco_cost_weights)
472    
473    checkpoint56c_post
474    o OBCS as control variables
475      - update ctrl_ad_diff.list, obcs_ad_diff.list
476      - remove balance of obcs controls from default
477      - fix index bug nobcs in ctrl_init
478      - fix dummy fields filen in ctrl_pack
479      - add dummy weights for obcs
480    o lsopt: comment out fort.94 output
481    o optim:
482      - remove unnecessary header files
483      - adjusted namelists
484      - add xerbla.F to Makefile
485    o exf:
486      - multiple modifications of exf_check_range
487      - unit change in exf_init_runoff from [m/year] to [m/s]
488    o mdsio:
489      - i/o-vector change debugLevel from debLevA to debLevB
490    
491    checkpoint56b_post
492    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
493      is called from DO_THE_MODEL_IO
494      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
495      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
496      - clean up PTRACERS_WRITE_TIMEAVE a little
497    o add another verification experiment that tests both the cfc-pkg and
498      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
499      reactive tendencies treated inline with regular timestepping
500    o testreport previously did a lousy job of comparing small numbers, so
501      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
502      implemented in the little c-progam tmp_cmpnum.c which is embedded in
503      testreport.
504    o ptracers_monitor: bug fix for MPI
505    
506    checkpoint56a_post
507    o GCHEM: finish reorganizating the package
508      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
509        (introduces another 3D-array for each passive tracer, but only if
510        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
511        gchemTendency is not needed because the timestep is done separately)
512      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
513      - GCHEM is now---more or less cleanly---separate from PTRACERS
514      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
515        so clear to me how that should be done in a general way.
516    o CFC: improve formatting of output in CFC_ATMOS
517    o PTRACERS:
518      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
519        that ALL experiments with ptracers enable can be checked. This makes
520        GCHEM_MONITOR obsolete.
521      - include a runtime parameter PTRACERS_monitorFreq that defaults to
522        monitorFreq
523      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
524    o add PTRACERS (PTR0[1-5]) to testreport output
525    o exf_check_range:
526      * default changed to .TRUE.
527      * will check values for niter0 if debLevA, every timestep if debLevB
528      * STOP in exf_check_range if 'out of range'
529      * range chosen generous to allow for potential extema
530      TBD: a version with stricter range
531           permitted range would be runtime parameters
532    o GMredi:
533      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
534      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
535      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
536    o GCHEM:
537      - move call to GCHEM_FORCING_SEP, so that it is now called before
538        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
539      - introduced a useGCHEM runtime flag and applied it everywhere.
540      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
541        this flag is now only visible within GCHEM-pkg routines.
542      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
543        be replaced by a 3D array that is computed before thermodynamics; for
544        this, the tracer ID iTracer had to be included into the parameter list
545        of ptracers_forcing
546      - set up forward_step to call gchem_forcing, that will replace
547        gchem_forcing_int in ptracers_forcing
548      - cleaning up
549    o small cleaning of exch2: remove files that are also in eesupp/src
550    
551    checkpoint56
552    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
553    o mnc: cleanup "full" files--fixes out-of-memory problem
554    o ECCO-GODAE
555      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
556      * fully merged and updated from SIO code
557        windstress sign change affects
558        - exf_inscal_[u/v]stress
559        - sign of xx_tau[u/v] adjustments
560        - signs in cost_scat
561      * ctrl_get_gen: avoid update of tau[u/v] for first few days
562      * natl_box_adjoint updated and compressed
563      * 2-level checkpoint switch added
564        (tested in EXP. 1 of natl_box_adjoint)
565      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
566    o SVD
567      * first complete, non-hacked version for SVD calculations
568      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
569        performed via direct access files admtlm_vector.it????
570        (via ctrl_[un]pack)
571      * optimcycle is used for ARPACK iteration counter
572        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
573      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
574        and add linear transforms where necessary
575      * controls are initial/final SST, SSS (can be extended; need to check
576        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
577    o mdsio: filename info to both stderr, stdout
578    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
579      from sign change
580    
581    checkpoint55j_post
582    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
583      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
584    o add consistent build directories and .cvsignore files to verification
585    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
586    o make all subroutines 30 or less characters in length for certain older
587      compilers to work (a thorough search only turns up two routines in
588      pkg/ptracers)
589    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
590      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
591    
592    checkpoint55i_post
593    o change arrays for total vertical diffusivity (2.D if explicit,
594      3.D if implicit) ; each ptracer uses its own background value.
595    o added mnc/NetCDF output capability to ocn_compon_interf
596      - added bits to verification/cpl_aim+ocn so that it can run on
597        ITRDA and other clusters without the mpirun "-wd" option
598    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
599      configuration
600    o give MNC the ability to create additional files rather than
601      exceeding a specified file size limit "MNC_MAX_FILESIZE"
602      - the default is just less than 2GB which is a practical limit
603        on many systems
604    o Compute the non-local term using either KPP vertical diffusivity (=default)
605       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
606    
607    checkpoint55h_post
608    o add verification test "vermix"
609    o remove all the *_ioinc flags and replace with the single global
610      outputTypesInclusive flag
611    o allow to set a vertical profile of vertical diffusivity for T & S
612    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
613    o useMNC moved from data.mnc to data.pkg
614    
615    checkpoint55g_post
616    o Renaming carbon AD experiments to comply with testreport conventions
617    o Updating adjoint of Held-Suarez hs94.1x64x5
618    o Fixing directives for non-ECCO forward_step, after ECCO directives
619      have been fixed to avoid recomp. of do_oceanic_phys
620      Works well for global_ocean.90x40x15,
621      but recomp. issue remains for carbon
622    o Updating adjoint output for natl_box_adjoint after
623      pkg/ecco has been modified (see taga c55d_post)
624    
625    checkpoint55f_post
626    o rename to timeave_init_fixed
627    
628    checkpoint55e_post
629    o some delicate re-shuffle of store directives to avoid one
630      extra call of do_oceanic_physics
631      affects ecco_the_main_loop.F, do_oceanic_physics.F
632      checkpoint_lev1_directives.h
633    o NB: this may break global_ocean adjoint temporarily,
634      but it is clear how to fix it. Will do later, need this now.
635    
636    checkpoint55d_post
637    o ECCO specific cost function terms (up-to-date with 1x1 runs)
638    o ecco_cost_weights is modified to 1x1 runs
639    o modifs to allow observations to be read in as
640      single file or yearly files
641    o enable to read exf forcing fields as either
642      single file or yearly files (flag useExfYearlyFields)
643    checkpoint55d_pre
644    
645    o switch between 2-level and 3-level checkpointing
646    o add ability of MNC to write local and "partial" (eg. 2D slices where
647      the full 3D field is never actually stored) arrays to NetCDF files
648      with the correct (that is, the complete multi-dimensional) set of
649      array indicies
650      - used in mom_vecinv() to write the diagFreq output
651      - tested (demonstrated) in verification/aim.5l_cs
652    o further mnc-ification
653      - add verification/lab_sea to the list with mnc setups
654      - fix undefined mnc v-names in cd_code
655      - add kpp to mnc output (both snapshot and timeave)
656    o non-hydrostatic code
657      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
658        in calc_gw.F
659      - defaults to viscAh
660      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
661        friction or Leith) in non-hydrostatic mode, as long as there is
662        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
663    o pkg/cost
664      extend simple cost functions to treat time mean quantities
665      (T,U,V) via cost_accumulate_state from cost_tile
666    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
667        be 2 times larger than the minimum size the advection scheme requires.
668        now get a perfect conservation of salt in advect_cs test-exp (updated)
669    o GGL90 (Gaspar's TKE mixed layer)
670      - add horizontal diffusion of TKE, requires exchanges in
671        do_fields_blocking_exchanges, horizontal diffusivity is zero by
672        default. In OPA there is no horizontal diffusion of TKE but the
673        mixing coefficients are computed from a horizontal average of TKE of
674        6 points or so. I think that diffusion has a little more physical
675        justification.
676      - clean up ggl90_calc in the hope of reducing memory usage (this hope
677        was in vain)
678      - mask tke-variable in ggl90_init
679    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
680    o fix biharmonic diffusion on CS-grid.
681    o more obcs stuff
682      - added obcs_external_fields_load as an alternative to the EXF-pkg option
683        for reading boundary values. This routine is called from
684        obcs_prescribe_read
685      - updated obcs_check
686      - changed sponge layer relaxation parameter units for days to seconds
687      - turned off sponge layer by default
688      - changed argument list of OBCS_CALC to myTime+deltaTclock
689      - fixed about 35 bugs in obcs_external_fields_load
690    
691    checkpoint55c_post
692    o obcs stuff
693      - new runtime flags useOBCSprescribe, useOBCSbalance
694      - re-arranged obcs_calc
695      - moved exf_getobcs to obcs_prescibe_read
696        obcs_prescibe_read is called after ORLANSKI stuff
697        and independent of it (executable can contain all).
698      - updated obcs_check
699      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
700        These may be necessary only if tangential velocities are
701        prescribed at OB, not sure, needs testing.
702    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
703      which simplifies the calls and passes the ifc check-bounds test
704    
705    checkpoint55b_post
706    o add a 2D scalar, Z location, exchange_2 routine.
707    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
708      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
709      affects advect_cs results (for the wrong reason): update output.txt
710    o use a more standard discretization for biharmonic viscosity ;
711     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
712      affects results of dome set-up: update output.txt
713    o fix gad_advection.F (CubedSphere part), back to version 1.23
714    o fix bug in mom_vi_del2uv.F (CubedSphere part).
715    
716    checkpoint55a_post
717    o merged code to
718      * prescribe/read time-dependent open boundaries
719        (works in conjunction with exf, cal)
720      * sponge layer code for open boundaries
721      * each boundary N/S/E/W now has its own CPP option
722        (healthy for the adjoint)
723    
724    checkpoint55
725    o up-to-date adjoint of previous breaks
726      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
727      - global_ocean_ebm: adjoint still needs fix (TLM ok)
728      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
729      - carbon: * remove tr1-related adjoint verification
730                * add ptracer as control variable
731    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
732      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
733    
734    checkpoint54f_post
735    o in verification/carbin/ remove experiment related to
736      ALLOW_PASSIVE_TRACER (array tr1 etc)
737      code_ad/ input_ad/ results_ad
738    
739    o add two new packages
740      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
741        + subject to optimization (memory)
742      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
743        + subject to reordering (many GOTOs in the original code)
744        + so far opps is called for every (i,j) point, and then operates in
745          the vertical; one may want to reorder the scheme in order operate in
746          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
747          fields)
748    o overhaul of IO so that we now have flags for MDSIO and/or MNC
749      - all verification tests compile and run with linux_ia32_g77
750      - defaults are compatible with current input files--nothing
751        should change if you were not previously using MNC
752      - MNC output has been added in numerous places (eg. timeave)
753        but there are still a few writes not yet do-able with MNC
754        (this is in progress)
755      - flags now allow for either/or/both use of MDSIO and MNC and
756        documentation will soon follow
757      - numerous small formatting cleanups for ProTeX
758    o add version info (via BUILD_INFO.h) to MNC and stdout
759    
760    checkpoint54e_post
761    o add two new packages
762      - pp81 (Packanowski and Philander, 1981), Richardson number and
763        stratification dependent mixing
764      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
765      - these scheme operate in a similar manner as KPP (without ghat, of
766        course), however there is only one diffusivity that is used for both
767        temperature and salinity (and passive tracers)ç
768    o add offline package
769    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
770      provided by Stephanie Dutkiewicz
771    o genmake2: add ability to search for C compilers and cleanup test output
772      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
773    
774    checkpoint54d_post
775    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
776    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
777      leading to additional shift by 5 days each year of integration
778       (i.e. leading to considerable offset over the years)
779    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
780    o start with no AB and no initial filtering (staggerTimeStep):
781      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
782    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
783      (external loading & cpl import/export stay in forward_step.F)
784    o update coupling interface to work with new staggerTimeStep
785    o change MDSIO ptracers_pickup.
786    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
787    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
788    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
789    
790    checkpoint54c_post
791    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
792      this affects (truncation error) output.txt of test-exp:
793       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
794    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
795    o change Qnet to always be the net heat flux, (+upward).
796      affects (truncation error) output of natl_box exp.: updated
797    o define the max number of passive tracers in PTRACERS_SIZE.h
798    o start to test mnc routinely in exp0
799    o add sea-ice loading (sIceLoad) as a new forcing field.
800    
801    checkpoint54b_post
802    o add testreport "-j JOBS" option for parallel builds (tested and pretty
803       impressive on Altix and Opteron systems)
804    o diagnostics can now write NetCDF files through the mnc package
805    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
806    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
807    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
808      affects (truncation error) output of lab_sea & natl_box exp.: updated
809    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
810    
811    checkpoint54a_post
812    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
813    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
814    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
815    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
816      + internal_wave (shift in writing cg2d_ini_res)
817    checkpoint54a_pre
818    
819    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
820      - modified verification/lab_sea and natl_box_adjoint accordingly
821    
822    checkpoint54
823    checkpoint53g_post
824    o prepare splitting of thermodynamics: store convect.counter in common block
825    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
826      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
827    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
828    o new parameter "nShapS": allow to treat differently S from T (nShapT)
829    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
830    o restore adjointability
831    
832    checkpoint53f_post
833    o modifications that affect AIM experiment results (update output.txt):
834      - no advection of S at top interface Nr (pkg/generic_advdiff)
835      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
836    o AIM pkg:
837      - include stability function into surf.Flux derivative relative to Tsurf
838      - calculate clear-sky radiation & surface temp. change (for diagnostics)
839    
840    checkpoint53e_post
841    o merged cylindrical coord configuration
842    o added rotating_tank experiment
843    checkpoint53e_pre
844    
845    checkpoint53d_post
846    o faulks upgraded: re-generate output.txt that have changed:
847       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
848    o Added Bryan and Lewis, 1979, vertical diffusivity profile
849    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
850    o added Sadourny discretization of Coriolis
851      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
852      - re-enabled use of omega3 (useAbsVorticity)
853    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
854      vector-invariant equations
855      - note: does *NOT* yet use same variable visc. for no-slip BC's.
856    o recoded the lateral boundary conditions for non-hydrostatic w, this time
857      hopefully without new bugs
858      - still to do: biharmonic friction for non-hydrostatic w
859    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
860    o regenerated output for global_ocean_ebm (using -ieee)
861    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
862      of mom_common/
863      - simple re-arrangement of instructions within computing loop
864    checkpoint53d_pre
865    
866    checkpoint53c_post
867    o new version of coupler for AIM+thSIce and Ocean models
868     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
869     - land: change Evaporation of snow
870     - aim with thSIce: fix bug in snow-precip.
871    o changes to calc_gw.F
872     - bug fix for w^2 term near the bottom boundary
873     - (hopefully) improve the lateral slip boundary condtions for use with
874        partial/looped cells
875      - because the bug fix changes two verification experiments anyway (exp5
876        and plume on slope), change the lateral boundary condition from half slip
877        to the value of no_slip_sides
878    o ebm package wasnt quite up to the parallel task. Fixed that.
879    o Adjoint of EBM package + verification
880      * TLM OK
881      * ADM not sufficient accuracy yet (needs further testing)
882    
883    checkpoint53b_post
884    o Commiting new energy balance model to repository
885      * package is pkg/ebm
886      * verif. is verification/global_ocean_ebm
887      * references are in ebm_driver.F
888    C      * X. Wang, P. Stone and J. Marotzke, 1999:
889    C        Global thermohaline circulation. Part I:
890    C        Sensitivity to atmospheric moisture transport.
891    C        J. Climate 12(1), 71-82
892    C      * X. Wang, P. Stone and J. Marotzke, 1999:
893    C        Global thermohaline circulation. Part II:
894    C        Sensitivity with interactive transport.
895    C        J. Climate 12(1), 83-91
896    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
897    C        Destabilization of the thermohaline circulation
898    C        by atmospheric eddy transports.
899    C        J. Climate 7(12), 1870-1882
900    o Will need long integration testing.
901    checkpoint53b_pre
902    
903    o created pkg/mom_common in preparation for variable viscosity code
904    o renamed and split ini_mnc_io
905    o pkg/land: only liquid water can diffuse or run-off
906    o AIM using land: soil wetness availability account for snow
907    o added printMapIncludesZeros to EEPARMS namelist
908    
909    checkpoint53a_post
910    o restore TAMC compatiility for exf_constants.h
911      (no usage of _d in .h)
912    o Additional storing in KPP in an attempt to fix
913      TAMC problem with adjoint of KPP code.
914      (no success...)
915      Identical code works fine with TAF.
916    o Fixed verification/natl_box_adjoint experiments.
917      Initial conditions for Experiments 4 and 5 are now
918      set to "SEAICE_initialHEFF=0", which is more reasonable,
919      and hence gives results closer to that of Experiment 2.
920      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
921    
922    checkpoint53
923    o stable checkpoint with up to date adjoint
924      TLM tests only run for 1st grdchk at the moment. Its unclear if
925      this is a code problem or a problem with resetting code for g_
926      variables that is being autogenerated wrong.
927      Otherwise:
928       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
929       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
930         are both still in chaos following their security messes.
931    
932    checkpoint52n_post
933    o various build (mostly genmake2) changes including:
934      - ability to build/run more easily within Cygwin and MacOS X
935      - more complicated Makefiles with a stronger dependence on Gnu Make
936    o pkg/seaice modifications
937      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
938        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
939        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
940      - changed proxy for geostrophic velocity and updated
941        verification/lab_sea/results/* accordingly
942      - removed ADI dynamic solver from pkg/seaice
943      - replaced all occurrences of 1/CSTICE or 1/CSUICE
944        they caused a segmentation fault under certain circumstances
945      - removed unused field WATR
946    o bug fix in exf-package:
947      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
948         now reflect that.
949    o small fixes in the cal-package:
950      - set reference date to first of January for the 'model'-calendar
951      - failing of cal_CheckDate in cal_FullDate now actually results in a
952        warning
953    o small modifications in exf-package to increase flexibility:
954      - change climtempfreeze from a constant to a runtime parameter that
955        is specified in data.exf_clim (default = -1.9)
956      - introduce runtime parameter windstressmax (default = 2.0) that is
957        specified in data.exf
958    o fix in pkg/thsice:
959      - update Evap (Tsf changes) to be consistent with Latent heat flux
960      - maintain snow precipitation unchanged (even if Tsf >=0).
961     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
962    
963    checkpoint52m_post
964    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
965      this does not change any of the results, because myIter=0 in swfrac always
966      lead to jwtype=2 (the default anyway), but the call makes little sense
967      as a default
968    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
969    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
970      atmospheric model (AIM) to use it ; add a "slab ocean" component.
971    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
972    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
973    o extending useSingleCpuIO option to work with new exch2 I/O format
974      - old-style, missing-tile I/O is still accessible by defining CPP
975        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
976    o monitor package can write to NetCDF files and/or STDOUT
977    o fix re-definition bug in MNC_GRID_INIT_ALL()
978    o doc/api_reference added
979      - a framework for building an API Reference Manual using all
980        the "protex" comments embedded in the code
981      - see pkg/generic_advdiff, pkg/mnc for examples
982    o MNC:
983      - make myThid the last argument for all subroutines
984      - new default for the grid files: NO halos
985      - add useMNC and other run-time flags
986      - separate per-file-group handling of the unlimited dimension
987      - early initialization of MNC w/ flags read at the eeboot stage
988        and lookup tables set in initialize_fixed
989      - write all MNC output to a freshly-created directory
990    o thermodynamics sea-ice (thsice) is now tested with testreport.
991    o test exp. advect_cs: use the standard cs32 grid ; update output.
992    o Added functionality to grdchk:
993      pick global i,j,k position (or nearest wet) where to perform check.
994    
995    checkpoint52l_post
996    o new land formulation:
997      a) use ground enthalpy as prognostic variable to ensure exact
998         energy conservation.
999      b) account for water temperature and for latent heat of freezing
1000         in all processes (rain, run-off, ground storage)
1001      c) compute surface and ground temperature implicitly.
1002    o aim_v23 modification for new land model:
1003      a) Treat separately land / ocean / sea-ice surface fluxes
1004         to allow implicit computation of land & sea-ice surface temp.
1005      b) add snow precipitation.
1006    checkpoint52l_pre
1007    
1008    o fix problem (when 1 tile is empty) in min/max monitor.
1009    o fix bug in timeAve (u,vZetatave in common block)
1010    o no restoring terms under ice for pkg/seaice
1011    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
1012    o bug fix for pkg/seaice pickups
1013    o change MNC call locations and add coordinate attributes
1014    o mask vorticity at the corner ; affects global_ocean.cs output
1015    o fix ini_curvilinear_grid ; test CS experiments with mpi
1016    o aim.5l_cs: modify sea-ice fraction input file ; update output
1017    o exf: Adding simple range check routine for exf fields after read
1018    
1019    checkpoint52k_post
1020    o removed top-level directory "diags"
1021      - we migrated these functions to pkg/timeave a long time ago
1022    o fixed bug introduced in pkg/monitor
1023    o accuracy ctrlprec = 32 insuffient for gradient checks using
1024      averaged fields (I/O via cost_averages)
1025      -> use ctrl.h in active_file*.F to control I/O precision.
1026    o paramter list of CALL ADTHE_MAIN_LOOP
1027    o added initial do_the_model_io to ecco
1028    o set all ...Freq to zero after cost_final
1029      taveFreq, dumpFreq, pChkptFreq
1030    o MAIN and ECCO differentiability restored
1031    
1032    checkpoint52j_post
1033    o fix nchklev in tamc.h for global_ocean...
1034    o Bringing flow and store directives up-to-date
1035    o Really weird thing!
1036      call do_the_model_io from the_main_loop with parameters
1037      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
1038      TAF places a faulty re-call of initialise_varia
1039      after cost_final call which should not be there!
1040    checkpoint52j_pre
1041    
1042    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
1043      error messages
1044    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
1045    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
1046      debug output
1047    o modfied mdsio_writefield.F to handle non-global files under exch2
1048    o update AIM Cubed-Sphere exp (aim.5l_cs):
1049      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
1050    o update AIM Equatorial Channel exp:
1051      use standard aim_v23 pkg and change the SST fields to be more realistic.
1052    o globalFile now works with exch2
1053    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
1054      mon_vort3.F to make exch2 friendly with >1 tile per cube face
1055    o limit timeave output for hi-res integrations
1056    
1057    checkpoint52i_post
1058    o removed CPP_EEOPTIONS.h from verification/*/code
1059    o updated the tiling for global_ocean_pressure
1060    checkpoint52i_pre
1061    
1062    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
1063      the old pkg/aim).
1064    
1065    checkpoint52h_pre
1066    o shortened offending lines in exch2_send_rx?.template
1067    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
1068    o genmake2: add build & execute test for NetCDF code
1069    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
1070      old grid files, moved CPP_EEMACROS.h to pkg/exch2
1071    o added useSingleCPUIO flag to monitor.F and mon_out.F
1072    o added temporary hack for sea-ice dynamics on the cube:
1073      metric terms are ignored and it is assumed that
1074      there is no sea-ice on cube faces 1, 2, 4, and 5.
1075    
1076    checkpoint52f_post
1077    o added exch2 cube routines to pkg/exch2
1078    o modified hs94.cs-32x32x5 to use it
1079    o added new grid files to hs94.cs-32x32x5
1080    checkpoint52f_pre
1081    
1082    checkpoint52e_post
1083    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
1084      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
1085    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
1086      to work with implicit vertical advection and AB ;
1087    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
1088    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
1089     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
1090    checkpoint52e_pre
1091    
1092    o fix bug in impldiff when Nr=1 or Nr=2.
1093    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
1094    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
1095    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
1096      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
1097    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
1098    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
1099    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
1100    
1101    checkpoint52d_post
1102    o re-tiled many expts to allow comparison in multi-processor mode
1103      - updated output accordingly
1104      - changed hs94.128x64x5 to use intial T from file rather than use the
1105        random number generator
1106    o add infrastructure in model routines for fizhi and gridalt packages
1107    o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
1108    o changes to permit hi-res, cubed-sphere, configuration
1109      - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
1110      - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
1111      - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
1112        of surface winds for the cube
1113      (A verification experiment, based on global_ocean.cs32x15, but with
1114       pkg/seaice turned on and with on-the-fly interpolation from the NCEP
1115       Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
1116       complete with example surface forcing files and matlab scripts to look
1117       at the output and compare it with that of global_ocean.cs32x15.)
1118    o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
1119       but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
1120       to conform to the common rule.
1121    o check-in the first version of the coupler + interfaces for multi-components
1122       set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
1123       - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
1124       - atmosphere: use pkg aim_v23 ; no sea-ice for now.
1125       - ocean and atmos. share the same horizontal grid (no interpolation).
1126       - exchanges between component and coupler is done in forward_step
1127    o new verification experiment, cpl_aim+ocn:
1128       coupled ocean - AIM atmosphere on cs32 grid.
1129    
1130    checkpoint52d_pre
1131    o surface flux time-av diagnostic modified for NLFS & RealFreshWater
1132    o add call to AIM pendant S/R in external_forcing & external_fields_load.F
1133    
1134    checkpoint52c_post
1135    o Fixing OPTIONS files for use of exf:
1136      - ALLOW_ECCO not needed
1137      - ECCO_CPPOPTIONS.h should not be included from
1138        EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
1139        as has been the case in the past
1140      - All cal/exf related options are currently set in
1141        single header file. Should remain so until we
1142        agree on a consistent new policy.
1143    o Removed all CPP options for cal package.
1144      cal has no more CPP options.
1145    o modified STOREs in GAD_ADVECTION
1146    o corrected key comp. for passkey
1147    
1148    checkpoint52b_post
1149    o new version: "thsice" of thermodynamic sea-ice pkg:
1150     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
1151     - modify fluxes but do not change theta directly;
1152     - light cleaning of bulk_force pkg (still needed with thsice).
1153     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
1154       + output_thsice.txt to test thsice & bulk_force pkgs.
1155    o put back grid & coriolis monitor output.
1156    checkpoint52b_pre
1157    
1158    o call "do_the_model_io" at the beginning (=> dump initial state)
1159    o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
1160    o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
1161      (need info on NUMBER_OF_PTRACERS)
1162    o missing PTRACERS headers in some routines
1163    o default tamc.h in pkg/autodiff supposed to crash
1164      to ensure proper customization
1165    
1166    checkpoint52a_post
1167    o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
1168      - moved surfaceTendencyTice from pkg/seaice to main code
1169      - subroutine FREEZE_SURFACE now limits only surface temperature
1170        and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
1171        => new output.txt for global_ocean.cs32x15 & global_with_exf
1172      - keep the old version of FREEZE for backward compatibility;
1173        global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
1174      - corresponding modifs for TAF directives
1175    o added surface flux output variables to TIMEAVE_STATVARS
1176    o time-averaged output for pkg/ptracers
1177    o fix problem with ECCO-related divided adjoint
1178      snapshot file was missing some ad-variables,
1179      but no warning issued by TAF
1180    
1181    checkpoint52a_pre
1182    o some bug fixes for #undef REAL4_IS_SLOW
1183    
1184    checkpoint52 = ecco_c52_e35
1185    o after testing adjoints of checkpoint51u_post
1186    
1187    checkpoint51u_post
1188    o this is the post-merge tag of the ecco-branch
1189      (needs another clean checkout and re-testing)
1190    o various natl_box_adjoint configs and results
1191      but no input fields
1192    o obcs adjoint not yet merged!
1193    o adding ECCO global 1x1 and 2x2 degree configs
1194    o updated/extended some store directives for seaice
1195    o pkg/ecco now containes ecco-specific part of cost function
1196    o top level routines the_main_loop, forward_step
1197      supersede those in model/src/
1198      previous input data.cost now in data.ecco
1199      (new namelist ecco_cost_nml)
1200    o in ctrl/ cleaned some cross-dependencies and updated CPP options
1201    
1202    checkpoint51t_post
1203    o this is the pre-merge tag of the ecco-branch
1204    
1205    checkpoint51s_post
1206    o cleanup: removed various obsolete #define-s
1207    o pkg/grdchk
1208      - renamed 'ph-grd 3' to 'grad-res'
1209      - merged from ecco-branch
1210        (remaining bug fixes for obcs gradient checks)
1211      - additional high-precision output for testreport
1212        (grep for 'precision_grdchk_result')
1213    
1214    checkpoint51r_post
1215    o cleaned up or removed CPP_OPTIONS.h files
1216    o updated results for some of the tests to reflect the new
1217      optfiles (-ieee: -O0 instead of -O3)
1218    
1219    checkpoint51q_post
1220    o cd_code:
1221      - moved cd_scheme.F -> cd_code_scheme.F
1222      - separate read_checkpoint from cd_code_ini_vars.F
1223      - separated cd_code part from write_checkpoint
1224      - updated AD_SOURCE, generated .flow
1225      - added CD_CODE_VARS.h to the_main_loop
1226      - Moving cd_code specific store dir.s to pkg/cd_code
1227    o ctrl package totally restructured
1228      - pack/unpack now optional and decoupled from
1229        xx_/adxx_ I/O
1230      - ctrl_pack/unpack cleaned
1231        (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
1232      - confined inclusion of AD_CONFIG.h to where necessary.
1233    o genmake2: changed AD dependencies from SRCFILES to AD_FILES
1234    
1235    checkpoint51p_post
1236    o create initial cd_code package
1237      - WARNING: the initialization of fields within packages
1238        is broken because INI_FIELDS (where READ_CHECKPOINT is
1239        called) is called *before* PACKAGES_INIT_VARIABLES.
1240        This seems to be backwards since
1241        1) its important to initially zero the entire field including
1242           the "halo" region
1243        2) zeroing needs to be done *before* reading pickup info
1244           and the pickup call might or might not happen in any
1245           particular run
1246      - this needs an overhaul for R2
1247    o cleanup verification/*/code/GMREDI_OPTIONS.h
1248    o cleanup testreport
1249    
1250    checkpoint51o_post
1251    o bringing AD-related verif's up to date with genmake2
1252      - carbon/
1253      - global_ocean.90x40x15/
1254      - hs.94.1x64x5/
1255      - (front_relax/ )
1256    o (more) consistent directory structure for AD-related verif.'s
1257    o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
1258    o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
1259    o bug fix in find_alpha.F for MDJWF:
1260      - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
1261        change rho -> rho-rhoConst
1262      - replace call find_rho to find_rhonum
1263    o initialisation of rFlx extended to full array (required by TAF)
1264      and shifted to thermodynamics
1265    o removed PTRACERS.h in ptracers routine
1266    o added surfacetendencyPtr to S/R parameter list pracers_forcing
1267    o Correcting initialisations for fVerU, fVerV.
1268    o helping TAF to recognize dependency on kUp for
1269      fVerU, fVerV
1270    o Replacing delZ by delR in pkg/ctrl/
1271    checkpoint51o_pre
1272    
1273    o undid all of cp51 pending some cleanups and discussion
1274    o added the [#include "AD_CONFIG.h"] statement to all files that need
1275       it for adjoint/tl #defines
1276     o re-worked the build logic in genmake2 to support AD_CONFIG.h
1277     o removed tools/genmake since it no longer works
1278    
1279    checkpoint51n_post
1280    o modifications to make FREEZE flux visible to pkg/kpp
1281      - moved surfaceTendencyTice from pkg/seaice to main code
1282      - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
1283      - subroutine FREEZE now limits only surface temperature
1284        (this means new output.txt for global_ocean.90x40x15,
1285         global_ocean.cs32x15, and global_with_exf)
1286    o added surface flux output variables to TIMEAVE_STATVARS
1287    
1288    checkpoint51n_pre
1289    o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
1290    o added [#include "AD_CONFIG.h"] to all files that use the following
1291      defines:
1292      - ALLOW_ADJOINT_RUN
1293      - ALLOW_TANGENTLINEAR_RUN
1294      - ALLOW_ECCO_OPTIMIZATION
1295    
1296    checkpoint51m_post
1297    o incorporating changes to get TAMC/TAF working in genmake2
1298      - added new TAMC/TAF targets to the Makefile
1299      - various cleanups related to package handling
1300      - these changes should have no impact on the forward model
1301    
1302    checkpoint51l_post
1303    o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
1304     - faster algorithm for cal_addtime.F
1305     - higher precision arithmetic, where needed
1306     - pkg/exf *startdate variables changed from calendar date to
1307       model integration time
1308    
1309    checkpoint51l_pre
1310    o add salt flux to forcing fields (used when salty sea-ice forms or melts)
1311    o enable to apply restoring on S & T only in a latitude band.
1312    o update output (external_forcing_surf modif. change truncation errors)
1313       global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
1314    
1315    checkpoint51k_post
1316    o change default to: useNHMTerms=.FALSE.
1317     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
1318       adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
1319     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
1320        exp1, ideal_2D_oce
1321     - change data file of oceanic exp (leave the results unchanged for now)
1322       exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
1323    o set gravitySign automatically according to the vertical coordinate used
1324      (and change sign: back to "logical" value: +1 when R increases downward)
1325    o added an include barrier to the default CPP_OPTIONS.h and
1326      removed the #include "PACKAGES_CONFIG.h" from it
1327    o fix a bug in mom_fluxform (from chk51j_post)
1328    
1329    checkpoint51j_post
1330    o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
1331    o adjusted some flow directives (dynamics, thermodynamics)
1332    o added cubed-sphere case to test cost function
1333    o heckpoint_lev?_directives.h now include
1334      pkg-specific directives, whenever those are enabled.
1335    o Moving pkg-specific flow directives to corresponding pkg
1336      Moving pkg-specific differentiation list to corresponding pkg
1337      Moving pkg-specific checkpoint-lev storing to corresponding pkg
1338      ---> conventions are
1339           - pkg_ad.flow
1340           - pkg_ad_diff.list
1341           - pkg_ad_check_lev?_dir.h
1342    
1343    checkpoint51i_post
1344    o merge of the branch-genmake2
1345      - knowingly breaks the older genmake
1346      - automatic generation of all ALLOW_${PKG_NAME} defines
1347      - new testreport supersedes older testscript
1348    o large number of package inclusion and header cleanups
1349    checkpoint51i_pre
1350    
1351    o new output for adjoin of global ocean vector invariant
1352    o fix for checkpoint of thermodynamic seaice and bulk_force
1353    o Steph gchem various cleanups
1354    
1355    checkpoint 51h_pre
1356    o fixed some single quotes
1357    o modify gchem pkg to be more versatile
1358    o modifications to clean up dic pkg
1359    o add pkg/cfc
1360    
1361    checkpoint51g_post
1362    o provide links for ARPACK and ADM*TLM
1363    o start removing verification/vero/
1364    o update AD-related stuff
1365      (in particular some IF-statements in model/src/ routines)
1366    o adding to verification/global_ocean.90x40x15/ adjoint of
1367      vector invariant setup
1368    
1369    checkpoint51f_post
1370    o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
1371    o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
1372      of tracer Green's fucntions for ocean inversion project.
1373    
1374    checkpoint51f_pre
1375    o Added on-the-fly spatial interpolation capability
1376        "USE_EXF_INTERPOLATION" to pkg/exf.
1377      - This is a temporary Cartesian-grid hack until
1378        the super-duper ESMF coupler becomes available.
1379      - See verification/global_with_exf/README for usage example.
1380      - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
1381        flags and modified pkg/seaice accordingly.
1382    o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
1383        and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
1384        non-local transport term.
1385    
1386    checkpoint51e_post
1387    o pkg/mom_vecinv:
1388      - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
1389      - add time-ave diagnostic of vorticity advection.
1390    o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
1391    o atmospheric geopotential: - include water vapor effect;
1392                                - use p^kappa in p* scaling.
1393    o land pkg: read initial state from files.
1394    o AIM : add stratospheric drag in the upper level
1395    
1396    checkpoint51d_post
1397    o change function ILNBLNK (=> last non-blank char.) to return zero
1398      (instead of the string length) when the string. char is empty
1399    o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
1400    o modif's to restore TAMC compatibility
1401      - avoid "_d" constructs in PARAMETER declarations
1402      - avoid interrupting lines by comment lines
1403    o Use cluster local disks for purely local I/O
1404      vs. globally visible disks needed for ctrl stuff
1405      (merged from ecco-branch)
1406      - new active_file_loc... and mdsio_..._loc routines
1407      - affected packages: autodiff, ctrl, grdchk, mdsio
1408    
1409    checkpoint51c_post
1410    o introducing integer flag debugLevel
1411      - debLevZero: suppress all output
1412      - debLevA: standard
1413      - debLevB: equivalent to current debugMode=.TRUE.
1414    o introducing pathname variable mdsioLocalDir for mdsio
1415      that can be specified at runtime
1416      (relevant for cluster I/O to local disk)
1417    `
1418    >>>checkpoint51b_post
1419    adjoint of ptracers
1420    o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
1421    o extended state in checkpoint_lev?, etc.
1422    o alternative ctrl/cost with tr1 or ptracer
1423    o new comlev1_bibj_ptracers
1424    o new ptracers.flow
1425    o made ptracers_forcing same as external_forcing_s
1426    o added verification for adjoint with ptracers
1427      - adm. grdchk fail so far
1428      - tlm. grdchk OK
1429      - checked tapelev/comlev recomputations: OK
1430    <<<checkpoint51b_pre
1431    
1432    checkpoint51a_post
1433    o added code for biogeochemistry package
1434      - new pkgs: dic, gchem
1435      - new subroutine in ptracers
1436    o modify code for biogeo packages
1437      - in model/src and pkg/ptracers
1438    
1439    checkpoint51
1440    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
1441      - autodiff, ctrl, exf, grdchk, seaice
1442      kept separate packages
1443      - cost, ecco, obcs
1444    o updating verification/internal_wave, verification/lab_sea
1445      (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
1446    
1447    checkpoint50i_post
1448    o Preparing next differentiable checkpoint and sync
1449      of MAIN vs. ecco-branch
1450      - 1st step: this one is differentiable
1451      - 2nd step: next(! not this) checkpoint will have updated packages
1452                  from ecco-branch)
1453    
1454    checkpoint50h_post
1455    o new package "land": provide surface BC for AIM.
1456    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
1457    o AIM: use true log-P extrapolation for near surface temp (= as in
1458        F.Molteni paper) ; update aim.5l_cs output.
1459    o New variable in PARM03 for more flexible pickups
1460    o somewhat cleaned package initialisation sequence for
1461      ctrl/ cost/ ecco/ in packages_... routines
1462    
1463    checkpoint50g_post
1464    o merged with release1_p17 (pkg/seaice and verification/lab_sea)
1465      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
1466      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
1467        made the default because of faster convergence than ADI
1468    
1469    checkpoint50f_post
1470    o exf totally restructured
1471      - replaced all exf_set_ routines by one generic exf_set_gen.F
1472        and made sure it's still differentiable
1473      - split exf_getffields.F into new exf_bulkformulae.F
1474      - exf_inscal_/exf_outscal_ suffixes consistent with field names
1475      - updated adjoint/makefile and relevant verif. accordingly
1476    
1477    checkpoint50f_pre
1478     o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
1479          + change Evap over land. (update aim.5l_cs output)
1480     o added missing .cvsignores and made uniform across expts
1481     o changed configuration of tidal_basin_2d expt
1482     o added pkg/debug functions for tracing code in fatal crashes
1483     o tidied pkg/monitor to use MONITOR_OPTIONS.h
1484     o new fn in pkg/monitor to stop model if solution grows too big
1485     o removed lots of single quotes from comments
1486    
1487    checkpoint50e_post
1488    o make KPP work with PTRACERS
1489     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
1490       nearly a copy of kpp_transport_s
1491     - there is no analogue to SurfaceTendencyS, so I have to use
1492       gPtr(of the surface layer) instead
1493    o add a new platform SunFire+mpi (SunFire 15000) to genmake
1494    checkpoint50e_pre
1495    
1496    checkpoint50d_post
1497    o change kpp output from multiple-record state files to single-record state
1498      files analogous to write_state.F
1499    o reduce the output frequency of cg3d-related stuff to the monitor frequency,
1500      analogous to the cg2d-related output.
1501    o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
1502      so that writing to internal file fn (with length 512) fails.
1503    checkpoint50d_pre
1504    
1505    checkpoint50c_post
1506    o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
1507    o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
1508    o add time-average diagnostic of U*V and vertical diffusive flux for theta.
1509    o bug fixed in convective adjustment diagnostic (multi-tile set-up).
1510    o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
1511    
1512    checkpoint50c_pre
1513    Merging from release1_p13:
1514    o bug fix for pkg/seaice dynamic solver
1515    o Added SEAICE_initialHEFF to pkg/seaice
1516    
1517    checkpoint50b_post
1518    o store u*,v* in gU,V instead of in guNm1,gvNm1
1519    o in order to put the momForcing out of the Adams-Bashforth:
1520      move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
1521      to timestep.F
1522    o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
1523    o re-generate output for highly sensitive test-exp:
1524       global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
1525    
1526    checkpoint50b_pre
1527    o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
1528    o corrected CPP option mismatch in exf_Bulk... functions for case
1529      #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
1530    
1531    checkpoint50a_post
1532    o Bug fix for merging between c50 and KPP.
1533      ikey was passed from thermodynamics to kpp_calc via
1534      common block rather than being recomputed in kpp_calc,
1535      in contradiction with new key itdkey.
1536      New key ikppkey created, and tamc.h headers updated.
1537    
1538    checkpoint50
1539    - 2nd step of merge with ecco-branch:
1540      merge changes in ecco-branch back into main trunk
1541    - bug fix in find_alpha
1542    - more storing in gmredi_calc_tensor.F, kpp_routines.F
1543    - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
1544    - merged some sliced AD support routines
1545    
1546    checkpoint49
1547    merged from ecco-branch:
1548    o exf:
1549      - Enable initialisation of forcing fields to constant
1550        (runtime) values.
1551      - in exf_getffields.F
1552        Reduce i-/j-loop to interior domain, discarding overlaps.
1553        That also fixes wrong TAF-key computations for key_1, key_2
1554        with bulf formulae.
1555      - exf_init.F modify #ifdef for exf_init_evap
1556      - exf_getffieldrec.F, ctrl_getrec.F
1557        The following INT-usages are not safe:
1558          fldsecs  = int(fldsecs/fldperiod)*fldperiod
1559          fldcount = int(fldsecs/fldperiod) + 1
1560        and were modified.
1561    o autodiff: checkpoint_lev...
1562      - updated storing for bulk formulae (some arrays were missing)
1563      - added state for seaice package
1564      - synchronized with main branch
1565    o DIVA:
1566      Modif.s in
1567      - the_main_loop.F
1568      - the_model_main.F
1569      and added cost_final_restore.F cost_final_store.F
1570      o With these changes, it is possible to fully separate
1571        the first forward run to compute the cost function (mdthe_main_loop)
1572        and adjoint runs over individual DIVA intervals (adthe_main_loop)
1573        into separate model executions.
1574        This enables better tuning of DIVA to given queue sizes.
1575      o Loss of cost function value in consecutive DIVA runs is
1576        fixed by storing to 'costfinal' file.
1577      o Appropriate call of ctrl_unpack/_pack,grdchk_main at
1578        beginning/end of adjoint integration is accounted for.
1579      The current changes apply to TAF-1.4.26.
1580      TAF has one remaining bug, requiring one manual change
1581      (see MITgcm manual).
1582    o cal: synchronized between MAIN and ecco-branch
1583    
1584    checkpoint48i_post
1585    o Changes to restore differentiability of code w.r.t. previous tag
1586      (mostly adding new routines to make list and replacing
1587      pressure by totPhiHyd).
1588    o Updated and merged grdchk package
1589      - has both ADM and TLM checks
1590      - works for single- and multi-proc.
1591      - output cleaned
1592      - worked successfully for parallel DIVA
1593    o genmake:
1594      - Adding -platform=SP4
1595      - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
1596    o Modif. for DIVA:
1597      ctrl_unpack should not be called in intermediate DIVA interval.
1598      (similar thing would apply for active files such as
1599      tbar, sbar, psbar, which should not be reinitialised;
1600      only relevant for ecco-branch)
1601    
1602    checkpoint48h_post
1603    o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
1604    o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
1605    o Added SEAICE_initialHEFF to pkg/seaice
1606    o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
1607    
1608    checkpoint48g_post
1609    --- EOS:
1610    o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
1611      store total Potential in totPhyHyd for diagnostics & EOS.
1612    o fix restart and overlap Pb when using Z-coord and EOS funct. of P
1613    --- Pressure/geopotential gradient:
1614    o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
1615    o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
1616      ( changes results of global_ocean_pressure )
1617    o NLFS + z-coord.: add eta*Rho' contribution.
1618    o accurate phiHyd when using interface-W at the middle between 2 centers
1619     ( changes results of ideal_2D_oce )
1620    o includes r* 2nd term in potential gradient.
1621    
1622    checkpoint48f_post
1623    Merging from release1_p12:
1624    o Modifications for using pkg/exf with pkg/seaice
1625      - improved description of the various forcing configurations
1626      - added basic radiation bulk formulae to pkg/exf
1627      - units/sign fix for evap computation in exf_getffields.F
1628      - updated verification/global_with_exf/results/output.txt
1629    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
1630      (SBO) core products, including oceanic mass, center-of-mass,
1631      angular, and bottom pressure (see pkg/sbo/README.sbo).
1632    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
1633      to avoid negative values in shallow regions.
1634      - updated verification/natl_box/results/output.txt
1635      - updated verification/lab_sea/results/output.txt
1636    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
1637    o Added useSingleCpuIO option (see PARAMS.h).
1638    o Updated useSingleCpuIO option in mdsio_writefield.F to
1639      work with multi-field files, e.g., for single-file pickup.
1640    o pkg/seaice:
1641      - bug fix in growth.F: QNET for no shortwave case
1642      - added HeffFile for specifying initial sea-ice thickness
1643      - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
1644    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
1645      kpp_transport_t.F, forward_step.F, and the_main_loop.F
1646    o pkg/seaice:
1647      - adjoint-friendly modifications
1648      - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
1649    
1650    checkpoint48e_post
1651    o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
1652    o dynamics: change definition of computational domain & adapt mom_fluxform
1653      accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
1654    o following exp works with Olx=Oly=2 (and pass through checkbounds option):
1655        adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
1656        exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
1657        global_ocean.90x40x15 global_with_exf global_ocean_pressure
1658        inverted_barometer solid-body.cs-32x32x1
1659      (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
1660    
1661    checkpoint48d_post
1662    o in preparation for r*:
1663     a) use pre-computed gradient of hydrostatic potential:
1664        changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
1665     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
1666        => affects results of glob_oce_pressure (different truncation error)  
1667      update output.txt of ideal_2D_oce & global_ocean_pressure
1668    
1669    checkpoint48d_pre
1670    o in preparation for r*:
1671      new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
1672      pass the 2 comp. of the grad. as arguments to momentum S/R.
1673      but for the moment, only used if it does not change the results.
1674    o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
1675    
1676    checkpoint48c_post
1677    Modifications in treatment of initial flux forcing controls
1678    to avoid extra storing of flux fields.
1679    
1680    checkpoint48c_pre
1681    o Added tidal_basin_2d experiment (currently 1D!)
1682    o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
1683    
1684    checkpoint48b_post
1685    o r* coordinate added in #ifdef NONLIN_FRSURF block.
1686     (modification to pressure gradient not yet implemented)
1687    o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
1688      (for U & V) that are used for vertical advection of momentum.
1689    
1690    checkpoint48a_post
1691    o In preparation for r*, use temp. array to compute vertical transport
1692       in flux-form momentum pkg. => change results of few test-exp.
1693      Update output of: exp4, exp5, front_relax, global_ocean_pressure,
1694                        lab_sea, natl_box & plume_on_slope
1695    
1696    checkpoint48
1697    o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
1698    
1699    checkpoint47j_post
1700    o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
1701    o moved adexch from forward_step to addummy_in_stepping
1702    o added exch in ctrl_map_...
1703    o aveFreq.=0. at end of cost_final to avoid overwrite in
1704      reverse checkpointing loop
1705    o Yet more changes in gmredi:
1706      * adgmredi_calc_tensor
1707        avoiding all recomputation of gmredi_slope_limit
1708      * adgmredi_x/y/rtransport
1709        added flag for excessive storing to avoid recomp. of
1710        u/v/rtans, dTdx/y/z
1711        -> this is not really necessary and very memory-consuming
1712      * adgmredi_slope_psi:
1713        consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
1714      * gmredi_slope_limit
1715        re-activated full calculation of taperfct for case 'ac02'
1716    o updating verification/ adjoints of carbon, global_ocean.90x40x15
1717    
1718    checkpoint47i_post
1719    o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
1720    o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
1721      default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
1722    o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
1723    o gmredi: fix few bugs.
1724    
1725    checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
1726    This will be a good checkpoint to plug into the ecco-branch.
1727    o few modif.'s to get latest version adjointed
1728      (mainly kick out code in ini_linear_phisurf)
1729    o modif's to run adjoint with exactConserv
1730    o case GM_BOLUS_ADVEC should be cleaned
1731      S/R gmredi_slope_psi should be cleaned
1732    o verification/carbon now has exactConserv=.TRUE.
1733    
1734    checkpoint47g_post
1735    o time-average AIM output: becomes independent from statvars time-average
1736      (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
1737    o After TAF bug fix:
1738      Tested adjoint of gmredi package.
1739      Tests were done with checkpoint47 rather than with latest
1740      checkpoint47f_post since the latter is broken for the adjoint
1741      verification/carbon/ contains both ADM and TLM gradient checks.
1742    Here they are, before they get changed/lost/stolen.
1743    Mostly modif.'s to fix numerical sensitivities.
1744    Gradient checks OK for
1745    - GM_taper_scheme:
1746      * clipping
1747      * ac02
1748      * linear
1749      * glw91
1750      * dm95
1751      * ldd97
1752    - GMREDI_OPTIONS:
1753      * GM_VISBECK_VARIABLE_K
1754      * GM_NON_UNITY_DIAGONAL
1755      * GM_EXTRA_DIAGONAL
1756      * GM_BOLUS_ADVEC
1757    in conjunction with data.gmredi parameters to be checked in
1758    in a few minutes under verification/carbon/code/
1759    
1760    checkpoint47f_post
1761    Merging from release1_p10:
1762    o modifications for using pkg/exf with pkg/seaice
1763      - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
1764        and SEAICE_EXTERNAL_FLUXES
1765      - pkg/exf CPP options EXF_READ_EVAP and
1766        EXF_NO_BULK_COMPUTATIONS
1767      - usage examples are Experiments 8 and 9 in
1768        verification/lab_sea/README
1769      - verification/lab_sea default experiment now uses
1770        pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
1771    
1772    checkpoint47e_post
1773    o created a tag prior to creating a branch
1774    
1775    checkpoint47d_post
1776    o fixed bug in the oceanic pressure coordinates code: vertical viscosity
1777      at the bottom boundary had an erroneous half slip boundary condition
1778    o added bottom drag and no slip boundary condition capabilities to
1779      oceanic pressure coordinates code
1780    o added new verification experiment global_ocean_pressure, this experiment is
1781      also described in the tutorial section of the manual
1782    checkpoint47d_pre
1783    
1784    checkpoint47c_post
1785    o Added a verification experiment for a global cubed-sphere ocean run
1786      -  verification/global_ocean.cubed32x32x30
1787      -  uses pkg/therm_seaice and pkg/bulk_forcing
1788    
1789    o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
1790    o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
1791      when using P-coordinate; only implemented for atmospheric config.
1792    o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
1793      NOTES: requires option NONLIN_FRSURF to be "#define".
1794    o update advect_xz/results/output.txt (left from checkpoint44g_post)
1795    
1796    checkpoint47b_post
1797    Merging from release1_p9:
1798    o pkg/seaice
1799      - removed GOTO's and added taf directives
1800      - double precision constants to reduce the g77 (Linux)
1801        to F77 (SGI) differences reported in release1_p8
1802    o tools/genmake
1803      - added SGI options
1804    o verification/testscript
1805      - updated to that of checkpoint47a_post
1806    o verification/global_ocean.90x40x15/input/eedata
1807      - modified for SGI f77 compatibility
1808    o verification/lab_sea
1809      - added description of sea-ice model
1810      - added missing matlab routines
1811      - added test of thermodynamics parallelization
1812    
1813    checkpoint47a_post
1814    o new pkg: aim_v23
1815     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
1816       for now, keep the same surface forcing as before.
1817     - Part-Cell implemented into AIM; check that Heat & Water are conserved
1818     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
1819     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
1820    o add diagnostic of surface correction term in monitor output
1821    
1822    o bulk_force and therm_seaice
1823    - Two packages:  bulk_force (Bulk forcing)
1824      and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
1825    - Earlier integration from Stephaine Dutkiewicz
1826      and Patrick Heimbach.
1827    - Two ifdef statements for compile time,
1828       ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
1829    
1830    checkpoint47
1831    differentiable version of checkpoint46n_post
1832    o bug fix in quasihydrostaticterms
1833    o * "clean" adjoint code (in terms of extensive recomputations)
1834        can now be obtained for all GMREDI options (i.e. for
1835        - GM_VISBECK_VARIABLE_K
1836        - GM_NON_UNITY_DIAGONAL
1837        - GM_EXTRA_DIAGONAL
1838        - GM_BOLUS_ADVEC )
1839      * However, wrong gradient check problem remains unsolved.
1840      * New CPP options have been introduced for different
1841        tapering schemes
1842    o external_fields_load now part of differentiation list
1843    o pressure needs multiple storing;
1844      would be nice to have store_pressure at beginning or
1845      end of forward_step, e.g. by having phiHyd global (5-dim.)
1846      (NB: pressure is needed for certain cases in find_rho,
1847      which is also invoked through convective_adjustment).
1848    o recomputations in find_rho for cases
1849     'JMD95'/'UNESCO' or 'MDJWF' are OK.
1850    o #define ATMOSPHERIC_LOADING should be differentiable
1851    o ini_forcing shifted to begining of initialise_varia
1852    o Incorporating QNVS line search routines into MITgcm
1853      (this is separate code, and therefore not under pkg)
1854      lsopt/, optim/
1855    o Updated verification/carbon/
1856      - #define GM_VISBECK_VARIABLE_K
1857      - GM_taper_scheme    = 'ldd97'    
1858    
1859    checkpoint46n_post
1860    Merging from release1_p8:
1861    o verification/natl_box:
1862      updating new external_fields_load routine
1863    o New package: pkg/seaice
1864      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
1865      The sea-ice code is based on Hibler (1979-1980).
1866      Two sea-ice dynamic solvers, ADI and LSR, are included.
1867      In addition to computing prognostic sea-ice variables and diagnosing
1868      the forcing/external data fields that drive the ocean model,
1869      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
1870      The implied surface heat flux is then stored in variable
1871      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
1872      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
1873      non-local transport term.  Because this call precedes model
1874      thermodynamics, temperature under sea-ice may not be "exactly" at
1875      the freezing point by the time theta is dumped or time-averaged.
1876      N.B.: fairly large differences in accuracy occur across
1877            different platforms/compilers; comparison between
1878            g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
1879            generated output gives:
1880       T           S           U           V
1881      C D M    c        m  s        m  s        m  s        m  s
1882      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
1883      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
1884      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
1885    
1886      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
1887    o GAD:
1888      - generated new common blocks to account for call of
1889        same gad routines with differing traceridentities
1890        (needed to modify tracerIdentity indices in GAD.h)
1891      - generated separate common blocks for case useCubedSphereExchange
1892        (Department of Futurology)
1893      - parameter lists to gmredi_?transport: added tracerIdentity
1894      - added new key indices to tamc.h
1895    o external_fields_load:
1896      - added this routine to TAF list
1897      - needed to make some common blocks global and additional storing
1898        along the same lines as exf package (checkpoint_lev?_directives.h)
1899    o exf:
1900      updated external forcing package
1901      - bug fixes carried over from ecco-branch
1902        (missing OBCS_OPTIONS.h in two routines)
1903      - enable easy to use "no forcing".
1904      - added exf I/O for atmospheric loading
1905      - added exf I/O for runoff data
1906      - transfered scaling between exf <-> MITgcm to exf namelist
1907    o Adding new verification experiment global_with_exf.
1908      This verification experiment is almost identical to the
1909      global_ocean.90x40x15 experiment, except that it uses
1910      the exf (and cal) package instead of the
1911      external_fields_load routine (cf README file).
1912    
1913    checkpoint46m_post
1914    o modified testscript to return -- when there are no lines of "%MON" output
1915    o added new flag "quasiHydrostatic" for QH mode
1916      and new routine quasihydrostaticterms()
1917    o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
1918      New routine: mom_u_coriolis_nh()
1919    o fixed sign of non-hydrostatic metric terms in u and v equations.
1920      Depend on correct sign of gravitySign.
1921    o added work.pc* to .cvsignore in aim directories using ifc
1922    o introduced flag for controllin non-hydrostatic metric terms
1923    o removed gravitySign from PARM04
1924    o switched to g77/ifc from pgf77 in aim experiments
1925    
1926    checkpoint46l_post
1927    o made convective adjustment work with pressure coordinates:
1928     - changed the direction of k-loop in convective_adjustment.F for the
1929       case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
1930     - adjusted the reference pressure k-index in convective_adjustment.F
1931     - adjusted the convection condition in convect.F (in analogy to
1932       calc_ivdc.F)
1933     - convective_adjustment no longer computes anything on the halos
1934     - removed the warnings about negative salinity from find_rho.F and
1935       find_alpha.F; instead the new routine look_for_neg_salinity, called
1936       at the beginning of find_rho, find_alpha, and find_beta, does a
1937       check of the entire slice, if CPP-option
1938       CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
1939    checkpoint46l_pre
1940    
1941    checkpoint46k_post
1942    o fixed the verification/global_ocean.90x40x15 experiment:
1943     - new bathymetry (the world according to A., JMC, and M.)
1944     - new initial fields and forcing fields (*.bin files)
1945     - new POLY3.COEFFS (for the next release one should switch to a full
1946       equation of state: JMD95P or MDJWF)
1947     - fixed several errors and redundancies in the data file
1948     - experiment uses looped cells
1949     - added matlab directory with diagnostic scripts for plotting of output
1950    
1951    o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
1952     - read AIM physics parameters from a file (data.aimphys)
1953     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
1954    
1955    checkpoint46j_post
1956    o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
1957    o move wVel computation at the end of the time step, in S/R integr_continuity
1958    o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
1959    o update timeave pkg for wVel diagnostic.
1960    checkpoint46j_pre
1961    
1962    checkpoint46i_post
1963    o Clean up AIM package (and keep the results unchanged):
1964      include CPP_OPTION and use IMPLICT NONE in all routines ;
1965      declare all the variables _RL ; use _d 0 for all numerical constants.
1966      use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
1967    
1968    checkpoint46h_post
1969    o cleaned up the use of rhoNil and rhoConst.
1970      - rhoNil should only appear in the LINEAR equation of state, everywhere
1971        else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
1972        and the dynamical equations are all divided by rhoConst
1973    o introduced new parameter rhoConstFresh, a reference density of fresh
1974      water, to remove the fresh water flux's dependence on rhoNil. The default
1975      value is 999.8 kg/m^3
1976    o cleanup up external_forcing.F and external_forcing_surf.F
1977      - can now be used by both OCEANIC and OCEANICP
1978    checkpoint46h_pre
1979    
1980     Added code to convert surface volume flux (fresh water) into
1981     a mass flux when using P coordinates in the ocean (OCEANICP).
1982     Note: It assumes you have set rho0=rhoConst=density of fresh water.
1983    
1984    checkpoint46g_post
1985    o Include a new diagnostic variable phiHydLow for the ocean model
1986      - in z-coordinates, it is the bottom pressure anomaly
1987      - in p-coordinates, it is the sea surface elevation
1988      - in both cases, these variable have global drift, reflecting the mass
1989        drift in z-coordinates and the volume drift in p-coordinates
1990      - included time averaging for phiHydLow, be aware of the drift!
1991    o depth-dependent computation of Bo_surf for pressure coordinates
1992      in the ocean (buoyancyRelation='OCEANICP')
1993      - requires a new routine (FIND_RHO_SCALAR) to compute density with only
1994        Theta, Salinity, and Pressure in the parameter list. This routine is
1995        presently contained in find_rho.F. This routine does not give the
1996        correct density for 'POLY3', which would be a z-dependent reference
1997        density.
1998    o cleaned up find_rho
1999      - removed obsolete 'eqn' from the parameter list.
2000    o added two new verification experiments: gop and goz
2001      (4x4 degree global ocean, 15 layers in pressure and height coordinates)
2002    checkpoint46g_pre
2003    
2004    checkpoint46f_post
2005    o Enable tangent linear (forward mode) gradient checks:
2006      - extended active file handling to g_... files
2007      - added TANGENT_SIMULATION to theSimulationMode
2008      - extended grdchk package accordingly
2009    o added tangent linear setup in verification/carbon/code_ftl
2010    o added adjoint setup in verification/front_relax/code_ad
2011    
2012    checkpoint46e_post
2013    o Added new equation of state -> MDJWF
2014      - EOS of McDougall et al., 2002, JAOT, submitted
2015      - caveat: the equation of state is only valid for a smaller (more
2016        realistic?) range of values than JMD95P/Z and UNESCO
2017      - added masks to the calculation of pressure in store_pressure
2018      - added more check values for density in check_eos (ini_eos.F), some of
2019        the old check values are out of the range of the MDJWF-eos, so don't
2020        expect perfect matches for those
2021    checkpoint46e_pre
2022    
2023    checkpoint46d_post
2024    o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
2025      'OCEANICP', also initialised field pressure correctly in ini_eos in the
2026      case of pressure coordinates. eosType='JMD95Z' in
2027      combination with buoyancyRelation='OCEANICP' now causes an error.
2028    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
2029      in find_alpha/beta.
2030    checkpoint46d_pre
2031    
2032    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
2033      so that JMD95Z and JMD95P give approptiate static stability in find_rho.
2034    
2035    checkpoint46c_post
2036    o Changes necessary for ocean in p-coordinates
2037     -  Added new buoyancy relation = 'OCEANICP'
2038     -  Added new parameters = gravitySign (this used to be contained inside
2039        the factor dRdZ which I added when we first switched to R coordinates).
2040     X GM/Redi is not compatible (yet)
2041     X bottom drag and no-slip need to be debugged.
2042    checkpoint46c_pre
2043    
2044    checkpoint46b_post
2045    o Added new equation of state -> JMD95Z and JMD95P
2046      - EOS of Jackett and McDougall, 1995, JAOT
2047      - moved all EOS parameters into EOS.h
2048      - new routines ini_eos.F, store_pressure.F
2049    o Added UNESCO EOS, but not recommended because it requires
2050      in-situ temperature (see JMD95)
2051    o Modified formatting for knudsen2.f in utils/knudsen2 and added
2052      unesco.f to be used with POLY3
2053    checkpoint46b_pre
2054    
2055    checkpoint46a_post
2056    o Added (atmospheric) pressure loading
2057      - new field in FFIELDS.h, etc...
2058      - new cpp flag ATMOSPHERIC_LOADING
2059    o Changed hFacC to _hFacC in calc_phi_hyd.F
2060    o Added SHORTWAVE_HEATING to some files for consistency
2061    checkpoint46a_pre
2062    
2063    checkpoint46
2064    further merges from release1_p5
2065    o new ctrl package
2066      - adopted from ECCO environment to enable optimization
2067      - added Eliassen Palm fluxes to controls
2068    o added Eliassen Palm flux controls to gradient check package
2069    o cost package
2070      - Compatible with new ctrl package
2071      - added Eliassen Palm cost hooks
2072      - modif's of existing cost functions
2073    o Adjoint-related bug fixes in kpp:
2074      - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
2075      - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
2076    o autodiff package
2077      - flow directives:
2078        + new for S/R do_the_model_io
2079        + enhanced for S/R checkpoint
2080        + new gmredi.flow
2081      - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
2082        disable adcommon.h/g_common.h by default.
2083      - fixed problem for adjoint of global_max
2084    o modified verification/carbon/
2085    o New setup for adjoint of global_ocean
2086    o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
2087    o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
2088    o incorporated hooks for sponge layer code (external_forcing.F)
2089    
2090    checkpoint45d_post
2091    o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
2092    o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
2093      (affects plume_on_slope "cg2d" output)
2094    o add new parameter deltaTfreesurf for free-surface time stepping
2095    o exchange gT,gS when using staggerTimeStep & GM & Oly<4
2096    o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
2097    o change phiMin in exp1 (to agree with documentation)
2098    o add new flags:
2099     - T,S forcing inside/outside Adams-Bashforth
2100     - turn off temp,salt advection and/or forcing
2101     - for each tracer, define internal flag for multiDimAdvection & A-B
2102    o monitor: change definition of KE to check conservation of Energy
2103    
2104    checkpoint45c_post
2105    o Removed f90 comments ("!")
2106    o Modified initialisations to enable exf package for MITgcm
2107      (without invoking ECCO_PACKAGE).
2108    o modifications to gradient check package (Martin Losch)
2109      - enable centered differences
2110      - modified format of standard output
2111    
2112    checkpoint45b_post
2113    o cleaned exchange calls in cg2d
2114    o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
2115    o included CPP option SINGLE_LAYER_MODE in thermodynamics
2116      to configure barotropic setup (Martin Losch)
2117    o moved some initialisations within bi,bj loop in dynamics
2118      (TAF flow dependency)
2119    o in initialise_varia, moved call packages_init_variables
2120      before convective_adjustment_init
2121      (corresponding adjustment of TAF tape initialisation).
2122    o in calc_diffusivity/calc_viscosity extended domain to full overlap.
2123    
2124    checkpoint45a_post
2125    o compute Rho over the whole domain (extend iMin,jMin indices)
2126    o specific exchange for X-slice domain (case Ny=1)
2127    o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
2128    o solve_for_pressure : set cg2d_x to zero where OBCS are applied
2129    
2130    checkpoint44h_post = checkpoint45
2131    o Fix to restore differentiability:
2132      place at which packages_init_variables is called in
2133      initialise_varia is crucial for reverse control flow.
2134    o modifications in GMRedi to enable stable adjoint
2135      (corresponding modif's in thermodynamics, dynamics)
2136    o added missing hook for sponge layer code in external_forcing
2137    o modified test cost functions
2138    o storing in gad_advection (plus removal of write(0,*)!
2139    o missing headers TR1.h added in convective_adjustment routines
2140    o errorMessageUnit set non-equal zero in eeboot
2141      (conflict on some platforms, e.g. IBM SP3)
2142    o modified carbon verif.
2143    
2144    checkpoint44h_pre
2145    o vertical grid option: allow to put the Interface at the middle between
2146      2 cell-centers ; replace delZ in pkg/kpp by drF.
2147    o GM Advective form: Tracers are advected using the residual transport (=
2148      Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
2149    
2150    checkpoint44g_post
2151    o fix surface correction term in multiDimAdvection (affects plume_on_slope
2152      results) ; ifdef missing in thermodynamics.F
2153    
2154    checkpoint44f_pre,checkpoint44f_post
2155    o added PTRACERS package
2156      This allows an arbitrary number of passive tracers to be integrated
2157      forward simultaneously with the dynamicaly model.
2158      + Implemented so far:
2159        - basic forward algorithm (time-stepping, advection, diffusion, convection)
2160        - I/O and checkpointing
2161        - GM/Redi  *but*  using the GM/Redi coefficient of Salt
2162      + Not implemented so far:
2163        - KPP
2164        - OBCS
2165      + No specific example supplied (yet) but global_ocean.90x40x15 has the
2166        necessary data.ptracer file. Simply use -enable=ptracers and uncomment
2167        line in data.pkg.
2168      + This package is disabled by default since it increases storage.
2169    
2170    
2171    o testscript: added -cleanup option
2172    o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
2173                 b) enable to filter 2D fields.
2174    
2175    checkpoint44e_pre,post
2176    o re-wrote convective adjustment to use pre-calculated weights
2177      Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
2178      Adds:    model/src/convective_weights.F, convectively_mixtracer.F
2179      Original calls to convect() still in place.
2180    
2181    chkpt44d_pre,post
2182    o added missing EXCLUDE_MONITOR flags
2183    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
2184      (incompatible typ in MIN/MAX expressions caused problems
2185      on IBM SP3)
2186    o in genmake added variable MAKEDEPEND
2187      plus resetting for case SunOS
2188    o added timer_stats.c routine for IBM SP3
2189    o removed variables in dynamics
2190    !!! I forgot to create tag chkpt44d_pre !!!
2191    !!! But chkpt44d_pre = chkpt44c_post    !!!
2192    
2193    o real fresh water flux implemented with non-linear free-surface.
2194    
2195    chkpt44c_pre,post
2196    o few fix (mask in shap_s2, EmPmR in external_field_load,
2197      USE_NATURAL_BCS in solve_for_P);
2198    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
2199    
2200    checkpoint44b_pre/_post
2201    o merge of relevant stuff from the ecco-branch:
2202      - genmake: removed $S64 overwrite for case SunOS
2203      - pkg/exf: update and corrections for field swapping and obcs
2204      - pkg/ecco: parameter lists for the_model_main, the_main_loop
2205                  harmonized between ECCO and MITgcm
2206      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
2207                      updated checkpointing_lev... lists for obcs
2208      - model/src: minor changes in forward_step, plot_field
2209                   added directive for divided adjoint in the_main_loop
2210      - pkg/mdsio: added mdsio_gl_slice
2211    
2212    o check parameters & config (chkpt44a_pre,post)
2213    o OBC and NonLin_FrSurf.
2214    
2215    checkpoint44
2216    o fix bug in mom_vi_del2uv
2217    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
2218    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
2219    o update AIM experiments (NCEP input files)
2220    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
2221    o added some stuff for AD
2222    
2223    checkpoint43
2224    o added two new advection tests
2225    o added global 4x4 degree ocean test
2226    o added test of H&S94 with free surface on cube
2227    o some final mods for gradient check, adjoint,...
2228    
2229    checkpoint42
2230      Fixed AD-related problems:
2231    o Store directives up-to-date with re-arranged Adams-Bashforth
2232      (mainly thermodynamics.F)
2233    o New store directives for multi-dim. advection schemes
2234      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
2235      * new common block and key passkey
2236      (mainly gad_advection.F)
2237    o Modified store directives for split of dynamics/thermodynamics
2238      for the case ALLOW_KPP
2239    o Cleaned argument list for timestep_tracer.F
2240    
2241    checkpoint41
2242    o re-formatted/added comments in prologues of key subroutines
2243      to work with protex
2244    
2245    checkpoint40
2246    o moved calc_gs, calc_gt and calc_tr1 back to model/src
2247    o added FLT (floats) package from Arne along with demo. experiment
2248    o re-arranged Adams-Bashforth scheme for tracers to allow easier
2249      implementation of forward-in-time forcing terms
2250    o more mods for non-linear free-surface including new variable
2251    o modified multi-dim method to work on cube
2252    o bug fix in KPP (from DM)
2253    
2254    checkpoint40pre9
2255    o added DST advection schemes
2256    o fix MPI bug on SGI's
2257    o modifications for non-linear free-surface
2258    o fixed conditionals for fixed flow/passive tracer only mode
2259    o added tension/strain form of stress tensor
2260    o changes to commenting of arguments for TAF/TAMC
2261    o added/updated many matlab scripts
2262    o added multi-dimensional advection method for tracers
2263      
2264    checkpoint40pre8
2265    o new package rw/
2266      Added method for dumping intermediate local arrays:
2267      mdsio_writetile - same as mdsio_writefield except works from inside
2268                        bi,bj loop
2269      mdsio_writelocal - same as mdsio_writetile except works for local
2270                         arrays
2271      write_local_r? - higher-level wrapper for mdsio_writelocal
2272      Controlled by diagFreq. Defaults to zero (ie. no dumps)
2273      Example given at end of mom_vecinv.F that dumps some local arrays.
2274    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
2275      control flux-form versus vector invariant code.
2276      Switch is runtime flag vectorInvariantMomentum (defaults to false)
2277      or genmake -DISABLE ...
2278    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
2279      (additional storing is now needed for case vecinv;
2280      currently nothing implemented to switch this storing off
2281      in case fluxform is used since no CPP flag available).
2282    
2283    checkpoint40pre7
2284    o bug fix in dynamics.F
2285      calc_viscosity called before k=1,Nr loop.
2286    o added some #ifdef's ALLOW_PASSIVE_TRACER
2287    o cleaned initialisations in ctrl_map_ini
2288      related to TAF
2289    
2290    checkpoint40pre6
2291    o split dynamics into thermodynamics & dynamics
2292    o corresponding split of calc_diffusivity into
2293      calc_diffusivity, calc_viscosity
2294      (kpp_calc_diff, kpp_calc_visc).
2295    o Added diffkr, kapgm to control variables
2296    o bug fix in gmredi_slope_limit for ldd97
2297    
2298    checkpoint40pre5
2299    o proper initialization of Adams-Bashforth time stepping
2300      + uses forward step for very first step of model (iter=0)
2301    o re-generated *all* output since almost all output is modified by this
2302      change (sorry but we've been putting this one off for about 2 years)
2303      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
2304        *not* regenerated since they are already out of date and I don't
2305        want to create the impression that they are suddenly working.
2306    o removed KAP stuff for DEC's
2307    o modified/added many .cvsignore files in */code and */input
2308    o added new expt "solid-body.cs-32x32x1"
2309      + this uses an alternative form of ini_curvilinear_grid.F which
2310        is not necessarily any better than the current one...
2311    
2312    checkpoint40pre4
2313    o added re-initialisations of utrans,vtrans,rtrans in
2314      calc_common_factors which are crucial for TAF.
2315    o extended iMin,jMin range for calc_common_factors,
2316      calc_diffusivity
2317    o added option ALLOW_PASSIVE_TRACER
2318    o a few minor updates and fixes
2319    
2320    checkpoint40pre3
2321    o created calc_gtr1.F for gad package
2322    o split the_main_loop and re-introduced forward_step
2323    o some recomputations of nIter0 for TAMC
2324    
2325  checkpoint40pre2  checkpoint40pre2
2326  o Updated to latest branch of AJA, JMC  o Updated to latest branch of AJA, JMC
2327  o Added gradient check package  o Added gradient check package

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