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revision 1.1018 by jmc, Sun Aug 24 22:03:51 2008 UTC revision 1.1319 by jmc, Sun Oct 24 21:35:13 2010 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/obcs:
8       writing sections with globalFiles=T does not work: add a STOP for this case.
9    
10    checkpoint62m (2010/10/21)
11    o pkg/seaice: vectorize seaice_solve4temp.F
12      - move iterations loops outside of i/j-loops
13      - requires 2D arrays for TB and effConduct
14      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
15        modified in this routine
16      - a little bit of clean up, adjusting indentation, etc.
17      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
18        performance and '**TWO' by '**2' (because TWO is a float),
19        replaced ONE, ZERO
20    o eesupp/src:
21       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
22    o pkg/seaice/seaice_growth.F
23      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
24      merging process. The merged routine has two branches, and one activates the 'evolution'
25      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
26      In summary, here is what the '10/10 revision' did consist of
27        part 1: seaice_growth.F revisions 1.71 to 1.75
28          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
29            The emphasis here was on improving readability (e.g. by trying to use meaningful
30            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
31        part 1.5:
32          - revising the lab_sea experiment to make it a more useful (i.e. stable
33            and representative of an actual model run). This was done by generating a
34            (winter) pickup to start from, switching back the main experiment dynamic
35            solver from evp to lsr, having one of the experiments use the free drift solution.
36        part 2: seaice_growth.F revisions 1.76 to 1.85
37          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
38          - Sorting out the various fields units and sign (set early on and reset at the end)
39            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
40            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
41          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
42            and simplifying logical expressions to further improve readibility.
43        part 3: seaice_growth.F revisions 1.86 to 1.89
44          - Re-organize the blocks of code more logically.
45          - Merging the '_if.F' pieces that add something new.
46    o pkg/thsice:
47      - vectorize thsice_solve4temp and thsice_get_exf.
48        Problem: thsice_solve4temp has an unvectorizable statement that
49        might also be problematic for TAF
50      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
51        does not change the verifcation experiment, but will change all
52        experiments that have this flag undefined (not tested in verification);
53        a little reorganization to save a few 2D fields and recomputations
54      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
55      - 2nd step:  fix some store dirs
56        o seems to work somewhat, i.e. using ifort but not g77
57        o likely cause are incomplete init. or recomputation
58        o start verification/global_ocean.cs32x15/input_ad.thsice
59    o pkg/obcs: add support for exch2
60      - the position of the boundary and prescribed values are specified using
61        a global domain with exch2 facets stacked
62        - in x for N,S boundaries (like W2_mapIO=-1)
63        - in y for E,W boundaries (so E,W boundaries do not overlap)
64    o pkg/mdsio: add support for writing global sections with exch2
65        file layout is as for obcs described above:
66        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
67        - for y-z sections, facets are stacked in y
68    o pkg/thsice:
69       - change a few routines for better vectorization: thsice_albedo.F,
70         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
71         not affected, but in particular the latter routine has changed
72         dramatically (not necessarily easier to read now).
73       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
74       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
75    o verification/lab_sea:
76      - overhaul of the forward model experiments. The main motivation
77        for this revision is that lab_sea has proven quite fragile (when
78        changing the sea-ice code, and switching platforms) to a point
79        when failures were very hard to attribute to specific code problems.
80      - the suspected reason for this fragility is noise amplification by evp so,
81        to start with, we decided to replace evp with lsr in the main experiment.
82      - the input.lsr experiment thus became obsolete and was removed.
83      - it was replaced with the input.fd experiment that uses an
84        analytical "free drift" solution as the ice velocity field.
85      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
86        will hopefully allow us to discriminate problems due to dynamic solvers
87        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
88        us to test additional options, along with the salt plume package.
89      - Finally a pickup was generated (at the end of a one year run) to
90        make the tests more representative of an actual model run. Previously
91        the tests starting point was a 1m thickness of ice everywhere.
92    o pkg/seaice:
93      - introducing S\R seaice_freedrift.F that compute the
94        analytical solution to an approximate ice momentum
95        equation (i.e. the simple stress/coriolis balance).
96      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
97        of the free drift velocity field, and enable its use.
98        To actually use the free drift solution as the model ice
99        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
100    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
101    
102    checkpoint62l (2010/10/04)
103    o pkg/seaice:
104      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
105      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
106       version (with USE_ORIGINAL_SBI undef);
107    o add hooks for new packages OASIS, the package will follow
108      (hooks exclude the seaice pkg for now)
109    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
110      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
111      rather than mdsio_readvector.F/mdsio_writevector.F, within
112      adread_adwrite.F to read/write adjoint-related tapes to disk.
113    o eesupp and pkg/mdsio: ALLOW_WHIO
114      Option to write/read 2D fields to files including tiles halos.
115      The main purpose is for adjoint related "tape I/O".
116      The secondary purpose is for debugging phases.
117      A word on those rather specifically intended purposes.
118      The code was meant to be stripped down to the bare minimum.
119      Typically, there is a unique and basic mapping to the global
120      buffer (tile by tile, then proc by proc, then level by level), and
121      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
122      meant to generate user friendly outputs of various shapes and forms.
123      Rather it is intended, for the knowledgeabale developers,
124      to be largely independent of the many mdsio options, to allow
125      outputs of tiles+halos in debugging phases and in adjoint runs,
126      and to allow some flexibility in tuning (adoint) I/O depending on each
127      file system behavior. With regard to tuning, most of the potential knobs
128      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
129      to specify directories, to specify the typical size of I/O calls, etc.)
130      are not yet included, and will be added if they prove useful.
131    o pkg/seaice:
132       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
133    o pkg/seaice:
134       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
135       code (seaice_budget_ice_if.F) which enable to recover old standard
136       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
137       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
138    o model/src (rStar):
139       use simple average (not area weighted) of rStarFac at U,V point when using
140       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
141       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
142    
143    checkpoint62k (2010/09/17)
144    o adjoint
145       * changed verification/global_ocean.cs32x15 ; adjoint now tests
146         Adams-Bashforth 3 + NLFS + RSTAR
147       * some more modifs required for ECCO-GODAE v4
148    o pkg/seaice
149       add SEAICE_AGE_VOL option to use volume instead of area for
150       integrating SEAICE_AGE
151    o model/src:
152       first check-in of sigma & hybrid-sigma coordinate code ; also includes
153       non-linear free-surface parts ; but pressure-gradient not yet coded.
154    o pkg/ptracers:
155       option for ptracer to convert Salt Relax into additional EmP.
156        tested in exp. global_ocean.90x40x15.dwnslp (update output)
157    
158    checkpoint62j (2010/08/25)
159    o pkg/ggl90:
160       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
161    o pkg/dic: car_flux.F, phos_flux.F
162      - reduce number of exp-calls in order to improve performance
163      - clean up a little (replace fields by their macros, etc., fix
164        typo in CPP-flag)
165    o pkg/ggl90: minor changes
166      - GGL90diffKrS was removed --> always use GGL90diffKr
167      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
168      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
169        (commented out for now)
170      - change in max/min operations to ensure that smoothing is ok
171      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
172      - always use diffKrNrT as background profile (i.e. never use diffKr field)
173    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
174    o pkg/dic:
175      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
176        vectorization
177      - small bug fix in insol for the unlikely case of a cartesian grid
178      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
179        + now vectorize, which also removes adjoint recomputations;
180        + replace integer maksp1 by _RL maskp1
181        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
182    
183    checkpoint62i (2010/07/21)
184    o pkg/flt:
185      - with OBCS: stop floats which enter the OB region
186    o model/src:
187      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
188        for implicit vertical advection.
189    o pkg/seaice:
190     - account for melting in seaice age evolution.
191     - remove double counting of seaice ridging effect on seaice age.
192    
193    checkpoint62h (2010/06/18)
194    o pkg/exch2:
195     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
196    o tools/genmake2
197      - remove "-pdefault" option: redundant with the use of "packages.conf";
198      - remove file pkg/pkg_default : set the default as a pkg group
199        ("default_pkg_list") defined in pkg/pkg_groups;
200      - fix for case pkg/pkg_depend is missing (was hanging before);
201      - add option "-pgroups" to specify a different pkg_groups than the default.
202    o verification/adjustment.cs-32x32x1:
203       add a "minimal" set-up test (code_min & input_min) which only compiles
204       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
205    o tools/genmake2
206      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
207      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
208    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
209      files are nearly the same anyway.
210      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
211       - redefinition of tau(i,i) (by a factor of ustar)
212       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
213       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
214       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
215       - replace
216         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
217         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
218         by
219         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
220         (changes results)
221       -> exf_bulkformulae v1.22,
222          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
223          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
224                    output.txt 1.63
225           offline_exf_seaice: output.seaicetd.txt 1.7
226           seaice_obcs: output.txt 1.10)
227      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
228       -> exf_bulkformulae v1.23,
229          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
230          and global_ocean.cs32x15.icedyn (only 11 matching digits)
231      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
232    o adjoint of exch-1:
233     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
234       (note: was already like this when using EXCH-2) and remove flow dir
235       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
236     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
237     - update pkg/exch2 diff list.
238    
239    checkpoint62g (2010/05/19)
240    o eesupp/src (exch-1):
241     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
242       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
243       (renamed to exch1_*rx_cube.F).
244     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
245       to call new exch1 S/R ; update Makefile and .cvsignore.
246     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
247       exch2_xy_rx later)
248      Note: after updating your code, need to run "make clean" in eesupp/src
249    o test experiment bottom_ctrl_5x5:
250       new output_adm.txt with fewer grdchk & less monitor output.
251    o model/src:
252      remove the call to ini_cori in initialise_varia.F (just keep the usual one
253       in initialise_fixed.F). More consistent with coriolis & horizontal grid
254       beeing treated in the same way (ini_grid is not called a 2nd time).
255    o pkg/exf:
256      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
257      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
258      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
259      - cosmetic changes to exf_bulkformulae.F to make it look more like
260        exf_bulk_largeyeager04.F
261    o eesupp/src (exch-1):
262      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
263      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
264        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
265        (even without using MPI).
266      - Message mode: move RecvAck setting (indicator of buffer being ready)
267        from send_put to recv_get S/R (was useless before, but not sure if
268        it's much more useful now);
269      - Switch the order of sync: MPI-proc 1rst and then threads;
270      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
271      - fix AD code for communication mode ='get' (but not used).
272    o model/src:
273      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
274      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
275    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
276    o pkg/ctrl: require a specific set of control variables and exf-flags for
277      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
278    o model/src:
279     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
280       1rst forward sweep, to avoid over-writing output files during recomputations
281       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
282     b) 2nd version:
283      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
284      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
285         writePickupAtEnd) + seaice & ptracers output;
286      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
287    o model/src:
288      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
289    o pkg/exch2:
290      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
291      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
292    o pkg/autodiff & exch2:
293      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
294      (for now, only if ALLOW_EXCH2 is defined).
295    o pkg/autodiff:
296      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
297        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
298       + clean-up comments (_RS is not always real*4)
299      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
300      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
301        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
302    o testreport (AD-tests):
303      no longer link files from dir "../input" (1rst link files from
304      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
305    
306    checkpoint62f (2010/04/29)
307    o model/src/the_main_loop.F:
308      adjust store directives for seaice evp and multicategory according to
309      pkg/ecco/the_main_loop.F
310    o adjoint:
311      global_sum_ad was incomplete (noted many times by many people ;)
312      nice description by Jean U. as follows:
313      * allreduce(var) in global_sum.F can be interpreted as
314        reduce(sum) followed by broadcast of sum.
315      * The adjoint of that is
316        sum(adjoint) followed by broadcast(summed adjoint value)
317        or in other words, allreduce(sum, adjoint vars)
318      We were missing the sum(adjoint)!
319      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
320      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
321      The fix should produce 16-digit accuracy between
322      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
323      multi-CPU single-tile (e.g. nSx=1, nPx-2)
324      We'll probably change this yet again shortly
325    o eesupp/src:
326      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
327    o pkg/icefront
328      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
329        specification of addmass array based on a 2D field, which is added
330        at bottommost wet level at each horizontal location.
331    o model/src:
332     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
333     layout; (not always compatible with delX,delY setting; commented out for now).
334    o pkg/exch2:
335     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
336     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
337    
338    checkpoint62e (2010/04/15)
339    o pkg/obcs:
340      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
341    o pkg/dic:
342      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
343        (note: not presently tested in any forward verification exp.)
344       update tutorial_global_oce_biogeo AD output file.
345    o pkg/exf:
346      - account for the variation of albedo as a function of zenith angle
347        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
348    o build_options:
349     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
350    o pkg/dic:
351      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
352      - use binary pickup file for restart;
353      - initialise atmos-CO2 box from dic_pCO2 parameter;
354      - fix multi-threaded.
355    o pkg/rbcs:
356     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
357       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
358     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
359       and update output.txt
360    o pkg/kpp:
361     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
362     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
363       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
364       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
365     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
366       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
367    o pkg/offline:
368      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
369      (bug was added in version 1.10 on 2007-08-23).
370    o pkg/offline:
371      - no need to specify periodicExternalForcing, etc ... to use offline pack
372      - offline input files no longer just single prec --> parameter offlineLoadPrec
373    o verification/lab_sea:
374      change AD test to multi-tile setup and update all 4 AD output.
375      NOTE: while cost function values remain very similar,
376      gradients are very different, although gradient checks are self-consistent
377      Should try to get to the bottom of this (cost function summation order?)
378    o pkg/dic:
379      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
380      a weakness of TAF that drops part of double precision in log10 derivative.
381      <= changes removed since problem has been fixed in current TAF version 1.9.71
382      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
383    o pkg/ecco:
384      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
385      update all 4 lab_sea AD output.
386    
387    checkpoint62d (2010/03/22)
388    o build_options:
389      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
390    o remove unbalanced quote (single or double) in commented line of source code
391      (may cause some warning with some preprocessor/makedepend versions).
392    o pkg/seaice:
393      fix seaice_model.F for adjoint (gael) and update AD results of experiments
394       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
395    o testreport:
396      add option '-runonly' (short: '-ro') to just do the run part (without make).
397    o eesupp: remove JAM communication code (obsolete).
398    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
399      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
400      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
401      (update also the output).
402    
403    checkpoint62c (2010/03/02)
404    o tools/build_options :
405       move (some) old optfiles from build_options/ to build_options/unsupported/
406    o model/src and pkg/exf
407       surface relaxation -- separating data and data.exf options
408       The point is to ensure that we specify the surface relaxation
409       either in data or in data.exf (but not half and half) and to
410       avoid an accidental relaxation to 0 (which happened if a time
411       scale was specified but the file name was left empty)
412    o model/src model/inc and pkg/mom_common
413       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
414       => addition to the viscosity field as computed by others schemes
415    o tools/build_options:
416      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
417        but keep the former optfile for few weeks for smooth transition
418    o pkg/ecco
419      - allow user defined cost function contributions
420            CPP: ALLOW_USERCOST_CONTRIBUTION
421            USAGE: compute contributions in cost_usercost_all.F
422      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
423          the two options are complementary.
424    o pkg/smooth
425      - migration from contrib to the main repository
426    
427    checkpoint62b (2010/01/26)
428    o pkg/monitor:
429      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
430        (in case someone forgot to update customized pieces of code)
431    o nonHydrostatic:
432      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
433      - add a simple 2-D experiment (short_surf_wave) to test it.
434    o pkg/icefront:
435       adding the shell of, and the hooks to, a new package that
436       will model melting and freezing of vertical glacier ice fronts
437    o momentum:
438      add diagnostics of momentum tendency from Hydrostatic pressure gradient
439       (without surf.pressure term: would need a 2nd filling since implicit term).
440    o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
441      two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
442      cannot deal with the former
443    o cleaning:
444      - remove all (except OpenAD) old TLM output from results_ad dirs.
445      - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
446      - comment out maskH definition (replaced by maskInC)
447    o pkg/monitor:
448      - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
449        & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
450    
451    checkpoint62a (2010/01/15)
452    o model/src:
453      - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
454    o pkg/diagnostics:
455      - add optional level number diagnostics (i.e., level number to be define
456        explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
457      - strictly check for valid parser-code(10) ;
458      - check if adding diag to the list from the right place.
459    o pkg/longstep:
460      - change parameters and fix tracer conservation with rstar/nonlinear free surface
461    o diagnostics:
462     - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
463       S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
464    o pkg/diagnostics:
465     - Add option for writing vertical integral (sum of selected levels) of an output
466        field instead of writing output field levels. Activate this option on a per
467        output-file basis, by setting the 2nd character of fileflag to 'I'.
468     - Add field-specific information relative to level integral in 3rd postion
469        of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
470        vertically (x level-thickness x hFac), "r"=same but without hFac.
471    o do_the_model_io:
472      - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
473        in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
474        writing pickups and stopping.
475    o pkg/diagnostics (for now, only with mdsio):
476      - write time information to meta file (and modify accordingly rdmds.m) :
477        time-averaged diagnostics output: write starting and ending time of the
478        time-averaging interval ; snap-shot diagnostics output remains unchanged;
479    o pkg/timeave:
480      - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
481        always Nr), now assumed to be equal to number of levels of averaged field;
482        only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
483    o pkg/sbo:
484      - fix ocean bottom pressure global-average & 2-D time-ave output (was
485        neither initialised nor filled).
486      - add starting iteration in suffix of global-average output file
487        (to avoid over-writing the file after a restart)
488      - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
489    o time-average:
490      - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
491        (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
492         ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
493        this fix DIC_COST cumulative-time array (previously: bi,bj,k)
494      - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
495      - fix missing accumulation for pkg/opps.
496      - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
497         (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
498      - fix initialisation of time-ave vars and do only full time-step increment
499        (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
500    o pkg/layers:
501      - use standard RW pkg S/R to write the output
502        and remove local write_fld version (which had a problem).
503      - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
504      - fix LAYERS_CALC argument list.
505    o pkg/timeave:
506      - store cumulative-time in a simple tiled array (drop the level index)
507      - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
508    o pkg/ocn,aim_compon_interf
509      - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
510    
511    checkpoint62  (2009/12/23)
512    o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
513        (was not previously tested in any other exp.)
514    o pkg/monitor:
515      - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
516        mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
517        (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
518      - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
519      - change del2 calculation.
520      - use interior masks (instead of maskH, <- to be remove).
521      - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
522    o mask & obcs:
523      - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
524      - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
525        (called after packages_init_fixed)
526    o pkg/obcs:
527      - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
528        Fixes bug in obcs+exf with nSx*nSy.GT.1
529      - fix multi-tile handling in obcs balance code
530    o nonHydrostatic:
531      - Implement AB-3 for non-hydrostatic vertical momentum ;
532        (change ordering of var. stored in pickup file when using NH)
533      - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
534      - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
535        (in prep. for new NH free surface form).
536    o pkg/obcs:
537      add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
538    o model/src:
539      fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
540    
541    checkpoint61z (2009/12/01)
542    o nonHydrostatic:
543      Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
544        a spurious source of energy in simple baroclinic adjusment test case.
545      Update all non-hydrostatic exp output.
546    o model/src (3-d solver):
547      Change again 3-D solver free-surface RHS term when exactConserv=T:
548        simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
549        (which was not the case with previous formulation).
550      To recover previous version, just reset "oldFreeSurfTerm" to previous value.
551      Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
552    o nonHydrostatic:
553      - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
554        for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
555      - change 3-D solver to work with r* (for now, only with linear free-surf.)
556      - add few debug diagnostics (cg3d_x, residual)
557    o model/src:
558      fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
559        update output of exp. global_ocean.cs32x15.viscA4
560    o update output of exp. global_ocean.cs32x15.icedyn after removing
561      #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
562    o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
563    o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
564      for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
565    o model: add Christopher Wolfe's implemetation of the single reduction cg2d
566      (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
567      runtime flag useSRCGSolver. Modify verification experiment global_with_exf
568      to test this code
569    o pkg/cd_code:
570      Change defaut D-grid time-stepping to get the same for D-grid momentum as for
571       C-grid momentum. D-grid velocity used to be stepped forward in time with
572       Adams-Bashforth only on surface pressure term. Tests show that using AB on
573       D-grid coriolis term improves stability (as expected from CD-scheme paper).
574      To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
575      Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
576       lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
577       tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
578      Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
579           global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
580    o pkg/obcs:
581     - fix bug in initialisation (broken since Oct 1rst modification)
582       for useOBCSprescribe without useEXF.
583    
584    checkpoint61y (2009/11/15)
585    o pkg/seaice
586     - change (once again) the discretization for the evp solver: rather than
587       squaring the averages of strain rates, average the squares to give
588       a better approximation to VP behavior (in simple test); this breaks
589       verification experiments that use EVP (lab_sea and lab_sea.hb87)
590        --> update outputs
591    o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
592      to improve vectorization of adjoint code on TARGET_NEC_SX
593    o verification/vermix:
594      - change vermix to a more "classical" 1d column with high vertical
595        resolution, seasonal heat flux forcing and constant wind forcing
596        --> update outputs
597    o pkg/seaice
598     - fix diagnostics of principal stress components for EVP
599     - add optional diagnostics of non-linear convergence for LSOR solver
600     - make maximum zeta a runtime parameter
601    o model/src (3-d solver):
602      Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
603       which consisted in removing the Surf. Non-Hydrostatic pressure from the
604       whole column and adding it to Eta (inspired from Casualli, 1999):
605       Only affects 3-D solver initial guess and only if using ExactConserv,
606       but tests did show a degradation of solver convergence. For this reason,
607       decide to disable this piece of code.
608       to recover previous version, just set zeroPsNH = exactConserv (line 78).
609      Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
610    o pkg/ggl90:
611     - fix previous modif (unfortunatly has not been documented here).
612    o pkg/seaice/autodiff:
613     - add CPP flag to include clipping of zeta in EVP code;
614       although clipping of zeta is not necessary for EVP and not recommended
615       it was done by default, now clipping is disabled by default
616     - modify computation and store zetaC/Z in seaice_evp for TAF
617     - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
618     - change seaice_calc_viscosities/strainrates for better
619       vectorization after AD by TAF
620     - rearrange common blocks in SEAICE.h once again for easier dumps of
621       adjoint output, adjust adcommon.h and g_common.h
622     - change flux form of default advection scheme for better vectorization
623       of adjoint code
624     - modify lab_sea/input.lsr to test the flux form of default advection
625       scheme
626    o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
627      transition in checkpoint61r)
628    
629    checkpoint61x (2009/10/19)
630    o adjoint: adding two new verification experiments
631      * tutorial_global_biogeo: an online dic sensitivity experiment
632        (work with G. Forget)
633      * tutorial_dic_adjoffline: an offline dic sensitivity experiment
634        (an update of the Dutkiewicz et al., 2006 paper)
635      Both use the same CO2FLUX cost function, but different controls
636      Gradient checks look good, but some recomp. could still be traightened out
637      Should add xx_dic control variable to test at some point
638    o model/src:
639      add run-time parameters to check and/or mask initial Temp & Salt
640    o pkg/ptracers:
641      apply zonal filter (if used) to all passive tracers
642    
643    checkpoint61w (2009/10/12)
644    o adjoint:
645      * update and finish work on adjoint of dic package (G. Forget)
646      * start adjoint of offline package
647      * bug fix for cube-sphere TLM code (active_file_g.F)
648    o tutorial_global_oce_optim:
649      now tested with 4 tiles (change data.grdchk and update output_adm.txt)
650      and add SIZE.h_mpi for MPI testing
651    o pkg autodiff
652     - fix bug in autodiff_restore
653     - make genmake2 remove comments and empty lines from ad_input_code.f in
654       order to reduce file size (new script file remove_comments_sed)
655    o allows to specify vertical profile of vertical viscosity (viscArNr)
656    o pkg autodiff
657      autodiff_ini_model_io: comment out writing of grid information to netcdf
658      files, because at this time the grid fields are a bunch of zeros
659      (this is analogous to ini_mnc_vars.F)
660    o pkg seaice/autodiff:
661     left-over from removing the 3-time-level fields:
662     - small rearrangement of common blocks (SEAICE.h)
663     - fix field declaration in order to get meaningful output in
664       adseaice.*.nc (adcommon.h)
665    o pkg obcs:
666     - go through NH code only if nonHydrostatic=T
667     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
668     - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
669       => Update output of experiment seaice_obcs
670     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
671     - fix NH+Orlanski restart (add wvel OBC value in pickup file)
672     - fix restart for useOBCSprescribe + useEXF
673    o pkg ctrl
674     - make obcs as control parameter work also with useSingleCPUio
675     - replace a few sny and snx by Ny and Nx to be consistent with
676       ctrl_set_globfld_x/yz.F
677    o pkg seaice
678     - re-introduce global field frWtrAtm for the case of
679       ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
680     - catch the case of an empty filename in seaice_cost_init_fixed.F
681    o pkg ecco:
682     - small bug fixes in the_main_loop
683      . fix order of monitor arguments
684      . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
685      . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
686        that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
687     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
688       imbalance diagnostics for wmean_h/sflux = 0
689     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
690     - catch the case of empty filenames in ecco_cost_init_fixed.F
691       and ecco_readparms.F
692     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
693       to make this statement meaningfull in ecco_cost_weights.F
694    o pkg zonal_filt:
695      - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
696      - when using rStar, filter uVel*hFacW instead of uVel
697       (tested without topography: fix a Pb of growing instability with NLFS)
698    o pkg/aim/thsice:
699     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
700      (works as SST restoring)
701    o pkg/thsice:
702     -add specific parameter for salt restoring in slab mixed-layer
703       (by default equal to the temperature restoring)
704    
705    checkpoint61v (2009/09/21)
706    o pkg/kpp:
707     -add double diffusive contributions as a hack, turned off by default
708      for now, and the code can be excluded with a CPP-flag
709      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
710     -add a verification experiments to "vermix" to test this code
711    o pkg/mom_common:
712      Move computation of length scales to mom_init_fixed.F (avoid recomputation
713      at each time-steps*levels).
714    o pkg/layers:
715      Created a new package for computing volume fluxes in temperature or
716      [not yet implemented] density layers, e.g. for calculating residual
717      overturning circulations.
718    o pkg/diagnostics:
719      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
720    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
721    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
722      To avoid mixing type (RS/RL) of input/output array argument,
723      replace single mixed-type array with a pair from each type (RS/RL).
724    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
725      is now implemented for all pkgs (previously only done for the main pickup)
726    
727    checkpoint61u (2009/08/25)
728    o pkg/obcs:
729      - change OB?eta from _RS to _RL and put them into a separate commen block
730      - add code to read OB?eta from a file via obcs_prescribe_read: the code
731        compiles and does not destroy any other experiments, the data is read
732        properly, but the code is not tested in actual applications
733    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
734      create a meaningful unit attribute for the time coordinate variable
735    o pkg/ebm: add plenty of missing "_d 0" ;
736       update results of experiment global_ocean_ebm (fwd + adjoint tests)
737      Notes: several pieces of code only works for (very) specific set up
738       (domain size, lat range, etc ...); should be documented & stop if one
739       of those assumptions is not meet.
740    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
741       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
742          and offline_exf_seaice (seaicetd + adjoint).
743    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
744       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
745        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
746    o few changes to pass when compiling with strick checking of arguments
747       across S/R (allow to find few bugs in S/R calls).
748    o pkg/seaice:
749     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
750       2d-fields, for slightly better performance
751    
752    checkpoint61t (2009/07/22)
753    o pkg/seaice:
754     - remove unused variables in seaice_evp
755     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
756    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
757       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
758       each processor opens a different file (a fix from Matt).
759    o cg2d:
760       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
761       this reduces number of EXCH calls by 2 when using exch2.
762       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
763       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
764    o pkg/thsice:
765       add code for Near Infra-Red albedo (from Jeff)
766       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
767    o ini_model_io:
768       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
769       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
770       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
771    
772    checkpoint61s (2009/06/30)
773    o pkg/exch2 (exch2_rxN_cube*):
774       remove last BARRIER (no need to synchronise after getting data from shared
775       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
776    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
777      and generate new output (for the 2 tests) using default rotationPeriod.
778    o pkg/exch2:
779      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
780        (was already the case with AUTODIFF_EXCH2 defined)
781      - add bj in exch2 arrays and S/R.
782      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
783        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
784    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
785      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
786        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
787      - verification experiment natl_box.longstep
788    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
789      allow different versions of ifort (8 or 9) and different versions
790       of mpi (mpich or mpich2) to be used with the same optfile.
791      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
792       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
793    o pkg/seaice:
794      fix previous modif (3-level field removed) for old-pickup reading
795    
796    checkpoint61r (2009/06/25)
797    o pkg/seaice:
798     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
799      1. introduce fields for time step (N-1)
800      2. do not use levels 2 and 3 anymore (but keep them)
801      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
802         includes changes to pkg/thsice/thsice_get_velocity.F,
803         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
804         pkg/obcs/obcs_apply_uvice.F.
805     - completely remove code for leap-frog time stepping for second order
806       advection
807     - adjusted adjoint accordingly;
808       gradient checks have improved by an order of magnitude!
809    
810    checkpoint61q (2009/06/22)
811    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
812     - the boundary conditions along open boundaries are unclear, because the
813       associated masks are set to zero and are thus treated as closed when
814       applying the slip-boundary conditions.
815     - move initialisation of grid variables from seaice_init_varia to _fixed
816    o adding doc/diags_changes.txt
817    o model/src:
818      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
819       to avoid "_diags" naming if no relation to pkg/diagnostics.
820      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
821       file and only call PLOT_FIELD_XYZ if debugMode=T.
822      remove few PLOT_FIELD_XY calls outside initialisation.
823      remove few unnecessary BARRIER.
824    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
825      of salt_plume package in Southern Ocean
826    o pkg/thsice:
827     - fix hOceMxL in overlap (needed for sea-ice advection);
828       update output of experiment global_ocean.cs32x15.icedyn.
829    o pkg/seaice:
830     - make the (placeholder-)tracer IceAge a little more meaningful
831      by avoiding ridging of age due to convergent ice flow
832     - add diagnostics for surface temperature, atmospheric and oceanic
833       heat flux, and atmospheric and oceanic ice growth
834    
835    checkpoint61p (2009/06/10)
836    o eesupp (global_max & global_sum):
837     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
838     - remove starting & endding barrier (no longer needed)
839    o pkg/mdsio, writelocal:
840       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
841       (remove the STOP): uses shared buffer IO to store data from all threads
842       and then let master-thread write nThreads tiles.
843    o pkg/mdsio (read/write field):
844     - tiled IO done in 1 piece (all levels at a time);
845     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
846     - multi-threaded: allow to read/write local (non-shared) array
847       (was already working with singleCpuIO ; now works also without);
848       => no longer needs barrier call after reading a file (added inside
849       mds_read/write field).
850     - move barrier calls outside gather/scatter_2d to mds_read/write_field
851    o pkg/obcs/exf
852      - exf_getffieldrec.F: add a few ". _d 0" and
853                            add code to catch the case fldperiod = 0.  
854      - obcs_precribe_read.F: change if statements so that they match
855                              the variable type (_RL)
856      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
857        exf_iprec) as part of namelist EXF_NML_01
858    o pkg/mdsio:
859      - read/write tiled (local) files: read/write 1-level tile chunk at a time
860        (instead of segment of length sNx); expected to speed up tiled IO.
861    o pkg/exch2:
862      - take buffer copy from/to array out of S/R exch2_send/recv into new
863        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
864        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
865      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
866      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
867        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
868        including Topology header file (and common blocks).
869      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
870        remove 2nd exch call in exch2_s3d_rx (no longer needed).
871      - document S/R arg. list (+ update some comments)
872    o pkg/seaice:
873      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
874        temperature and humidity over sea ice based on climatological values.
875      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
876        of LSR (this change is expected to change the results slightly because now
877        it uses slightly difference moduli from the second last LSR solution, but
878        that is more consistent with the stress computations; this part of the code
879        is not tested in the verification experiments)
880      - fix diagnostics for flux of ice in case of B-grid
881      - turn strain rates eij and press into global fields within global
882        common block in SEAICE.h for more straighforward diagnostics
883      - fix diagnostics for principal stress components, press, zeta, eta
884        to give something meaning full
885    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
886      new output (all 4 tests) using default rotationPeriod.
887    o pkg KPP:
888      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
889      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
890        and normal grid from 1 to Nr)
891    o Fix computations of L4rdt in mom_calc_visc.F
892    o eesupp:
893      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
894      should be called before a "stop" if we know that all process are going
895      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
896    
897    checkpoint61o (2009/05/26)
898    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
899    o model/src/ini_curvilinear_grid.F:
900       compute angleSin/CosC when they are not read from a file
901    o pkg/seaice:
902       add pseudo time stepping for LSOR
903    o pkg/exch2:
904       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
905    o pkg/seaice:
906       Adding separate sea ice albedo, drag coefficients, and HO in Southern
907       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
908    o SingleCpuIO:
909       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
910    o pkg/seaice:
911       put exchanged variable in (local) common block for MPI+Multi-Threads
912       to work (necessary with exch1, and for now with exch2 too).
913    o verification: to get more experiments tested with mpi, mth and mpi+mth,
914      change tiling of:
915       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
916       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
917      update output of exp:
918       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
919       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
920      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
921                       (note: output.txt generated on faulks using only 1 tile)
922    o eesupp & mdsio (SingleCpuIO):
923     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
924       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
925       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
926     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
927     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
928       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
929    o pkg/exch2:
930     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
931       read parameter file "data.exch2" if it exists; otherwise try default regular
932       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
933     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
934       with new code (not to be used, just as a backup solution).
935     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
936       in utils/exch2/input.
937    
938    checkpoint61n (2009/05/12)
939    o eesupp & mdsio (SingleCpuIO):
940      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
941        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
942        receive real*4 array (instead of real*8) to read/write 32.bit files.
943        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
944         and remove new mapping S/R)
945    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
946      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
947        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
948        when using exch2. Add S/R to map global io-buffer to global model array.
949      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
950    
951    checkpoint61m (2009/04/29)
952    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
953      and add 3 other S/R for other types (R4,R8,RS).
954      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
955    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
956     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
957     - reduce number of macro definitions (keep only those which are used);
958       can always call directly the corrresponding S/R if needed.
959     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
960       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
961     Fixed wrong type of arg in:
962       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
963       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
964     To fix: global_sum of var in common block is wrong (multi-threaded) in:
965       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
966     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
967    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
968      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
969    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
970    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
971      edges are closed (zero depth); might happen with "blank tiles";
972      for now, disabled if using OBCS.
973    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
974      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
975    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
976      to reduce length of 1.D array print in STDOUT.
977    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
978      + use 48 tiles (16x8): this will allow to test "blank tiles".
979    o start to test MPI + multi-threaded (change testreport to skip tests
980      where number of tiles do not match).
981    o genmake2: add option "-omp" to turn on Open-MP ;
982      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
983    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
984      and keep the original tile numbering. Note: compatible with old
985      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
986    
987    checkpoint61l (2009/04/07)
988    o Overlaps had been forgotten in calculating ijk keys : fixed
989    o fix cyrus makedepend for gcc 4.4
990    o experiment fizhi-cs-aqualev20:
991      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
992      and generate new output. Note: new output is much closer to the old
993      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
994      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
995    o pkg/fizhi:
996     - change to avoid indices going deliberately over array-bounds
997     - remove unnecessary MPI stuff
998     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
999     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
1000       does not go over array-bounds and therefore returns reliable output.
1001     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
1002       this S/R has 4 output arguments, which are used inside "get_alarm";
1003       when it is called with the same variable "ndum" in place of several
1004       output arguments, this produces weird side effect inside "get_alarm"
1005      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
1006       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
1007       address) and produces error.
1008    o tools/gemake2: (March 27-29 2009)
1009      with option "-mpi": link *_mpi files from "MODS" dir (this is what
1010      testreport does).
1011    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
1012    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
1013       update lab_sea.lsr & lab_sea.salt_plume results
1014    o pkg/seaice:
1015      Major overhaul of the LSOR solver: change discretization from original
1016      finite differences to finite volume. The old routine is still in the
1017      file seaice_lsr.F and can be turned on with the CPP-flag
1018      SEAICE_OLD_AND_BAD_DISCRETIZATION
1019      Along with this change, the discretization of the strain rates is changed.
1020      The same flag turns on the old discretization in seaice_calc_strainrates.F
1021      All verification experiments with seaice are affected (except for
1022      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
1023      results by setting the above flag.
1024      Further changes involve changes in defaults:
1025      - ALLOW_FLOODING is defined and turned on by default
1026      - SEAICEadvSnow = .true. is now the default
1027      - SEAICEadvSalt = .true. is now the default
1028      - SEAICEadvAge  = .true. is now the default
1029      - SEAICE_clipVelocities  = .false. is now the default
1030                                         (as per J. Zhang's recommendation)
1031      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
1032        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
1033      - seaice_growth: replace computation of UG by a simple copy from wspeed
1034    
1035    checkpoint61k (2009/03/18)
1036    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
1037      seaice_lsr: fixed a few metric terms,
1038                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
1039                  add more debugging diagnostics
1040      seaice_evp: removed superfluous many metric terms of FV discretization
1041                  of stress divergence
1042                  affects lab_sea, lab_sea.hb87
1043      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
1044                  of stress divergence for non-evp solver
1045                  (this part is not tested anywhere)
1046      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
1047                  they were effectively only half slip
1048                  affects lab_sea.hb87
1049      updated all relevant verification experiments (except lab_sea//output_adm.txt
1050        which was left over, but fails at level 7 & 6)
1051    
1052    checkpoint61j (2009/03/17)
1053    o pkg/seaice: turn a few hard wired parameters into run time parameters
1054    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
1055      time in seconds as promised by the usints in seaice_monitor and exf_monitor
1056    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
1057      that are not cubed-sphere grids
1058    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
1059    o pkg/ctrl:
1060      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
1061    o non-hydrostatic (calc_gw.F):
1062      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
1063      update output of exp. global_ocean.cs32x15.viscA4
1064    o remove backward compatibility for thetaMin,phiMin
1065      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
1066    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
1067      interpolated wind field not only for curvilineargrid=.true., but also
1068      for a rotated grid (rotateGrid=.true.)
1069    o pkg/exf: add capability to bypass interpolation for runoff
1070      by setting yet another CPP-flag
1071    o eesupp/src, B-grid exchange:
1072      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
1073    o autodiff
1074      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
1075      allows to switch to single-prec common blocks;
1076      corresponding switch occurs in tamc.h, integer isbyte
1077      TAF store directivs "byte" and "kind" seem equivalent;
1078      Most tamc.h have been updated correspondingly.
1079    
1080    checkpoint61i (2009/02/13)
1081    o autodiff:
1082      fix autodiff_sore/_restore indices for obcs
1083      (spotted by I. Hoteit, M. Mazloff)
1084    o pkg/autodiff, pkg/ctrl:
1085      Add flag to reduce all tapelev I/O to single-prec.
1086      In data.ctrl set
1087        doSinglePrecTapelev = .TRUE.
1088    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
1089      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
1090    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
1091      real fresh water flux (not yet)
1092    o pkg/mdsio & rw:
1093     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
1094     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
1095    o pkg/flt:
1096     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
1097       init_fixed & ini_varia.
1098     - clean-up & simplify linear interpolation S/R:
1099       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
1100     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
1101     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
1102     - add vert. coordinate & horiz. indices to output files.
1103     - change vertical position in initial condition, from index to depth [m].
1104     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
1105       (easier to get to a curvilinear grid) ; delX,delY no longer used.
1106    o pkg/ggl90: a few modifications:
1107     - fix bottom boundary condition, and interpolation of KappaE
1108       near top and bottom
1109     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
1110     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
1111     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
1112    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
1113      (maintain temporary backward compatibility, until next checkpoint)
1114    
1115    checkpoint61h (2009/01/27)
1116    o pkg/diagnostics with "periodic averaging diagnostics":
1117      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
1118    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
1119    o pkg/obcs: fix loop ranges for balancing code
1120    o pkg/flt:
1121     - improve criteria for finding which tile owns a float.
1122     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
1123    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
1124      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
1125      with ocean biogeo)
1126    o pkg/flt:
1127     - do some cleaning and fix the restart ;
1128     - add output.txt in flt_example/results to get this pkg tested.
1129    o genmake2: add an EXTENDED_SRC option and flag.
1130       for now, cannot be turned on on command line (only through genmake_local)
1131    o pkg/mdsio: read/write vector:
1132     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
1133     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
1134       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
1135     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
1136      (drop to 4 digits matching for grad). But this test does not look very
1137      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
1138    
1139    checkpoint61g (2008/12/29)
1140    o pkg/flt:
1141      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
1142       + make OPTIONS file more standard.
1143      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
1144      - fix _BYTESWAPIO CPP-Flag
1145      - standard reading of file-parameter "data.flt"
1146      - fix argument list of S/R FLT_RESTART
1147      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
1148    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
1149    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
1150      a still unfixed compiler/optimization bug
1151    
1152    checkpoint61f (2008/11/21)
1153    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
1154      update results of global_ocean.cs32x15.icedyn test.
1155    o move getcon.F from model/src to pkg/fizhi.
1156    o pkg/exf: add parameter for extrapolation of temp up to the surface
1157       and option to prevent negative evap (in bulk_largeyeager04 only).
1158    o Prather Advection scheme: fix tracer conservation for divergent flow
1159      (e.g., when using NonLin Free-Surface).
1160    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
1161    o gmredi (Visbeck-variable-K):
1162     - add more parameters to Visbeck-variable-K.
1163     - use a 5 points average for dSigmaR in Visbeck-K calculation
1164       (more "homogenous": same stencil and same weights as in dSigmaH)
1165     - update output of ideal_2D_oce experiment.
1166    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
1167      (#undef REAL4_IS_SLOW)
1168     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
1169       coordinate variable
1170     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
1171       (surface forcing fields), removes some of the functionality
1172     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
1173     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
1174       probably not all: copy _RS surface flux fields to RL field before
1175       calling DIAGNOSTICS_FILL
1176     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
1177       real*4 (CALL EXCH_*_RS) versions.
1178     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
1179       (generate new output).
1180    
1181    checkpoint61e (2008/10/23)
1182    o gmredi (Visbeck-variable-K):
1183      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
1184      - change computation of Visbeck-K where Slope > Smax :        
1185        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
1186        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
1187    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
1188      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
1189    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
1190    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
1191      does not become too large (to avoid precision problems in implicit-diffusion
1192      solver); update ideal_2D_oce output.
1193    o pkg ggl90:
1194      - in ggl90_cal.F: compute only one set of visc/diff, used to
1195        step forward TKE/T/S/momentum
1196      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
1197        have Prandlt =1)
1198    o gmredi (fm07):
1199      - add lower limit on Transition layer thickness + lower limit on 1/lambda
1200      - allow to set few more params from data.gmredi
1201    o pkg ggl90:
1202          - add missing sqrt(2) factor in computation of mixing length
1203            scale in ggl90_calc.F
1204            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
1205    
1206    checkpoint61d (2008/09/25)
1207    o adjoint modifs
1208      - adapt to new field rhoInSitu
1209      - allow to revert from StoreDynVars2D, StoreDynVars3D
1210        to individual fields
1211        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
1212    o store 3-D (in-situ) density in commom block (DYNVARS.h)
1213     - save 1 rho computation.
1214     - no longer modify T & S inland when using down_slope pkg.
1215    o gad_som : allow to switch to SOM advection for T & S without corresponding
1216      pickup files (using new S/R: MDS_CHECK4FILE).
1217    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
1218      (for useSingleCpuIO to work in multi-threaded)
1219    o pkg/shelfice:
1220     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
1221       with SHELFICEtopoFile in data.shelfice
1222     - move code for reading ice shelf topography and modifying hFacC into separate
1223       subroutines of the shelfice package
1224     - separate initialisation of "fixed" and "variable" variables
1225     - kTopC is not (yet) replaced by kSurfC, although this is possible
1226    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
1227    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
1228      and rename:
1229      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
1230      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
1231    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
1232    
1233    checkpoint61c (2008/08/30)
1234  o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"  o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
1235    to add mass source/sink of fluid in the interior (3-D generalisation    to add mass source/sink of fluid in the interior (3-D generalisation
1236    of oceanic real-fresh water flux).    of oceanic real-fresh water flux).
# Line 21  o change FIND_RHO to FIND_RHO_2D : Line 1248  o change FIND_RHO to FIND_RHO_2D :
1248    pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.    pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
1249  o new pkg: cheapaml  o new pkg: cheapaml
1250    
1251  checkpoint61b  checkpoint61b (2008/08/05)
1252  o exch2:  o exch2:
1253    change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)    change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
1254    - no longer depend on the order sequence (N,S,E,W).    - no longer depend on the order sequence (N,S,E,W).
# Line 36  o exch2: Line 1263  o exch2:
1263     more intuitive this way) ; rename/remove some variables.     more intuitive this way) ; rename/remove some variables.
1264   - change utils/exch2/matlab-topology-generator & code_mods accordingly.   - change utils/exch2/matlab-topology-generator & code_mods accordingly.
1265    
1266  checkpoint61a  checkpoint61a (2008/07/29)
1267  o exch2/matlab-topology-generator:  o exch2/matlab-topology-generator:
1268    fix bug in index bounds for N-S internal exchange (hard to tell if this    fix bug in index bounds for N-S internal exchange (hard to tell if this
1269    had any effect on the solution).    had any effect on the solution).
# Line 45  o pkg/mnc: small fix in mnc_handle_err: Line 1272  o pkg/mnc: small fix in mnc_handle_err:
1272  o testreport: modify syntax of awk, so that it works also with  o testreport: modify syntax of awk, so that it works also with
1273    awk, and not only with nawk and gawk    awk, and not only with nawk and gawk
1274    
1275  checkpoint61  checkpoint61 (2008/06/24)
1276  o autodiff  o autodiff
1277    Change default for TAF usage by removing argument '-nonew_arg'    Change default for TAF usage by removing argument '-nonew_arg'
1278    This changes TAF subroutine argument list (ordering of active var.)    This changes TAF subroutine argument list (ordering of active var.)
# Line 56  o autodiff Line 1283  o autodiff
1283    Tested TAF version is 1.9.22    Tested TAF version is 1.9.22
1284    N.B.: exch2 hand-written adjoint code currently not TAMC compatible    N.B.: exch2 hand-written adjoint code currently not TAMC compatible
1285    
1286  checkpoint60  checkpoint60 (2008/06/19)
1287  --->>> This is the last checkpoint for which generating the adjoint  --->>> This is the last checkpoint for which generating the adjoint
1288  --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"  --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
1289  --->>> by default.  --->>> by default.
# Line 81  o bridging the gap between eddy stress a Line 1308  o bridging the gap between eddy stress a
1308    The key modifications are in model/src/taueddy_external_forcing.F    The key modifications are in model/src/taueddy_external_forcing.F
1309    pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F    pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
1310    
1311  checkpoint59r  checkpoint59r (2008/05/29)
1312  o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array  o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
1313    from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);    from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
1314    fix option to read coriolis(@ cell-corner) from files with CS-grid.    fix option to read coriolis(@ cell-corner) from files with CS-grid.
# Line 112  o pkg/ptracers: add second-order moment Line 1339  o pkg/ptracers: add second-order moment
1339    (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)    (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
1340    and requires a fortran 90 compiler    and requires a fortran 90 compiler
1341    
1342  checkpoint59q  checkpoint59q (2008/05/06)
1343  o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)  o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
1344     (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)     (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
1345  o Refresh tutorial_global_oce_biogeo, notably:  o Refresh tutorial_global_oce_biogeo, notably:
# Line 147  o thsice pkg: Line 1374  o thsice pkg:
1374    - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos    - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
1375    --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice    --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
1376    
1377  checkpoint59p  checkpoint59p (2008/04/10)
1378  o gchem / dic / cfc :  o gchem / dic / cfc :
1379    - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);    - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
1380    - add new parameter files: "data.dic" & "data.cfc" ;    - add new parameter files: "data.dic" & "data.cfc" ;
# Line 173  o in mom_calc_visc, fix average value of Line 1400  o in mom_calc_visc, fix average value of
1400    bottom ; only used with variable horizontal viscosity and non-hydrostatic.    bottom ; only used with variable horizontal viscosity and non-hydrostatic.
1401    also fix diagnostics VISCAHW & VISCA4W.    also fix diagnostics VISCAHW & VISCA4W.
1402    
1403  checkpoint59o  checkpoint59o (2008/03/07)
1404  o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).  o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
1405  o change the loop ordering in most gad_*_adv_x.F to improve vectorization:  o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
1406    move a few statemens out the main loop into separate loops    move a few statemens out the main loop into separate loops
# Line 214  o pkg/ctrl: Line 1441  o pkg/ctrl:
1441      introducing a generic routine (ctrl_map_ini_gen.F).      introducing a generic routine (ctrl_map_ini_gen.F).
1442    - Modification of ctrl_bound/adctrl_bound handling control vector bounds.    - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
1443    
1444  checkpoint59n  checkpoint59n (2008/02/09)
1445  o pkg/diagnostics: for large number of diagnostics, store diagnostic mate  o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
1446    number in dedicate array "hdiag":    number in dedicate array "hdiag":
1447    - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST    - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
# Line 268  o pkg/seaice: add a new flag SEAICEuseTE Line 1495  o pkg/seaice: add a new flag SEAICEuseTE
1495    for now this is only available for the C-grid code and also within    for now this is only available for the C-grid code and also within
1496    #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code    #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
1497    
1498  checkpoint59m  checkpoint59m (2008/01/14)
1499  o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)  o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
1500    and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature    and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
1501  o gad_som : fix flux output (& diagnostics) to have same units as other    o gad_som : fix flux output (& diagnostics) to have same units as other  
# Line 286  o pkg/obcs and pkg/seaice: Line 1513  o pkg/obcs and pkg/seaice:
1513  o pkg/salt_plume: added various options for salt plume depth  o pkg/salt_plume: added various options for salt plume depth
1514    criterion and for vertical distribution of the salt    criterion and for vertical distribution of the salt
1515    
1516  checkpoint59l  checkpoint59l (2007/12/18)
1517  o pkg/ptracers: new version of ptracers pickup:  o pkg/ptracers: new version of ptracers pickup:
1518    read meta file and write only fields which are needed to restart.    read meta file and write only fields which are needed to restart.
1519    ( same logic as main pickup file ; also using pickupStrictlyMatch )    ( same logic as main pickup file ; also using pickupStrictlyMatch )
# Line 308  o no longer write pickup from THE_MODEL_ Line 1535  o no longer write pickup from THE_MODEL_
1535  o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL  o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
1536    or U/VICE from U/VWIND before computing U/VSTRESS    or U/VICE from U/VWIND before computing U/VSTRESS
1537    
1538  checkpoint59k  checkpoint59k (2007/11/30)
1539  o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between  o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
1540    dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.    dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
1541  o fix un-initialised variable problem (in mom_vecinv & shap_filt):  o fix un-initialised variable problem (in mom_vecinv & shap_filt):
# Line 330  o pkg/ptracers: Line 1557  o pkg/ptracers:
1557    use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).    use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
1558    to-do: fix pkg/diagnostics when large number of diagnostics are defined.    to-do: fix pkg/diagnostics when large number of diagnostics are defined.
1559    
1560  checkpoint59j  checkpoint59j (2007/11/09)
1561  o in pkgs: dic, obcs, offline, rbcs:  o in pkgs: dic, obcs, offline, rbcs:
1562    standard way to compute coeff. for time interpolation between 2 time reccords    standard way to compute coeff. for time interpolation between 2 time reccords
1563    which retains full precision (& make results less dependent on compiler).    which retains full precision (& make results less dependent on compiler).
# Line 373  o pkg/mdsio & pkg/rw: Line 1600  o pkg/mdsio & pkg/rw:
1600  o added open boundary conditions capability for seaice  o added open boundary conditions capability for seaice
1601      HSNOW, HSALT, UICE, and VICE      HSNOW, HSALT, UICE, and VICE
1602    
1603  checkpoint59i  checkpoint59i (2007/10/21)
1604  o adjoint:  o adjoint:
1605    * fix multiDimAdvection adjoint    * fix multiDimAdvection adjoint
1606      (partial recomputation problem by TAF for fVerT(:,:,kDown)      (partial recomputation problem by TAF for fVerT(:,:,kDown)
# Line 414  o change units of EmPmR (inside the code Line 1641  o change units of EmPmR (inside the code
1641    Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).    Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
1642    Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).    Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
1643    
1644  checkpoint59h  checkpoint59h (2007/09/29)
1645  o pkg/exf:  o pkg/exf:
1646    - improve vectorization by moving if-statement out of loops in    - improve vectorization by moving if-statement out of loops in
1647      exf_mapfields, exf_radiation      exf_mapfields, exf_radiation
# Line 447  o pkg/thsice: Line 1674  o pkg/thsice:
1674  o testreport: change AD testing : check against results/output_adm.txt  o testreport: change AD testing : check against results/output_adm.txt
1675    using same scripts as for forward test.    using same scripts as for forward test.
1676    
1677  checkpoint59g  checkpoint59g (2007/09/17)
1678  o adjoint testing: in preparation for changing testreport:  o adjoint testing: in preparation for changing testreport:
1679    - output format: cost and grad written on separated lines    - output format: cost and grad written on separated lines
1680    - ad output results in directory "results" (instead of "results_ad")    - ad output results in directory "results" (instead of "results_ad")
# Line 492  o pkg/cd_code: add brackets in multiple Line 1719  o pkg/cd_code: add brackets in multiple
1719    global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,    global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
1720    ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.    ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
1721    
1722  checkpoint59f  checkpoint59f (2007/08/21)
1723  o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)  o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
1724  o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in  o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
1725    a bounded range (in forward mode)    a bounded range (in forward mode)
# Line 523  o pkg/seaice Line 1750  o pkg/seaice
1750  o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update  o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
1751     output of global_ocean.cs32x15.thsice .     output of global_ocean.cs32x15.thsice .
1752    
1753  checkpoint59e  checkpoint59e (2007/07/26)
1754  o exch2: new S/R that only use the cube-tracer (center-position) exchange:  o exch2: new S/R that only use the cube-tracer (center-position) exchange:
1755    for B-grid vector (not yet tested) and C-grid vector (<- only used    for B-grid vector (not yet tested) and C-grid vector (<- only used
1756    when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).    when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
# Line 553  o pkg/seaice: Line 1780  o pkg/seaice:
1780    * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option    * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
1781    * applied OBCS T/S mask to HEFFM sea ice mask    * applied OBCS T/S mask to HEFFM sea ice mask
1782    
1783  checkpoint59d  checkpoint59d (2007/06/21)
1784  o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array  o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
1785   for {PKG} state variables, and called from DO_STATEVARS_DIAGS.   for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
1786   (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)   (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
# Line 599  o pkg/seaice: Line 1826  o pkg/seaice:
1826     It is turned off by default (=-1.), because it changes the results.     It is turned off by default (=-1.), because it changes the results.
1827   - make it possible to read AREA from a file, too.   - make it possible to read AREA from a file, too.
1828    
1829  checkpoint59c  checkpoint59c (2007/06/04)
1830  o add S/R and diagnostics for oceanic mixed-layer depth  o add S/R and diagnostics for oceanic mixed-layer depth
1831  o move GMRedi call after all vertical mixing schemes (including KPP)  o move GMRedi call after all vertical mixing schemes (including KPP)
1832  o pkg/thsice:  o pkg/thsice:
# Line 632  o adjoint: Line 1859  o adjoint:
1859    Storing is now bundled into large arrays to optimized I/O    Storing is now bundled into large arrays to optimized I/O
1860    (and second step in cleanup of the_main_loop)    (and second step in cleanup of the_main_loop)
1861    
1862  checkpoint59b  checkpoint59b (2007/05/16)
1863  o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):  o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
1864    - export/import (between ocean & coupler) fields needed for ocean DIC.    - export/import (between ocean & coupler) fields needed for ocean DIC.
1865  o pkg/seaice:  o pkg/seaice:
# Line 703  o pkg/seaice Line 1930  o pkg/seaice
1930  o OpenAD  o OpenAD
1931   - changed verification/OpenAD to full baroclinic setup (including GM/Redi)   - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
1932    
1933  checkpoint59a  checkpoint59a (2007/05/01)
1934  o pkg/seaice: some parameter clarifications and a little bit of clean up  o pkg/seaice: some parameter clarifications and a little bit of clean up
1935  o pkg/thsice: rename run-time parameters:  o pkg/thsice: rename run-time parameters:
1936     himin       -> hIceMin     himin       -> hIceMin
# Line 745  o pkg/seaice: fix bug in evp solver, whi Line 1972  o pkg/seaice: fix bug in evp solver, whi
1972  o pkg/kpp: add code to have mixing in shelf ice caverns  o pkg/kpp: add code to have mixing in shelf ice caverns
1973    - add myThid to all kpp routines (long overdue)    - add myThid to all kpp routines (long overdue)
1974    
1975  checkpoint59  checkpoint59 (2007/04/19)
1976  o pkg/exf:  o pkg/exf:
1977    - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &    - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
1978      ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid      ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
# Line 771  o pkg/thsise Line 1998  o pkg/thsise
1998    - 2nd set of modifs for thsice adjoint in conjunction with exf    - 2nd set of modifs for thsice adjoint in conjunction with exf
1999  o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)  o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
2000    
2001  checkpoint58y_post  checkpoint58y_post (2007/04/15)
2002  o Added capability for latitudinal dependence of Bryan and Lewis, 1979  o Added capability for latitudinal dependence of Bryan and Lewis, 1979
2003    vertical diffusivity, similar to that in MOM4; turned on using    vertical diffusivity, similar to that in MOM4; turned on using
2004    #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using    #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
# Line 787  o ice dynamics (pkg/seaice) with thsice Line 2014  o ice dynamics (pkg/seaice) with thsice
2014         - better when using non-linear advection scheme (not yet fully tested)         - better when using non-linear advection scheme (not yet fully tested)
2015         - can also be used in atmospheric set-up (for now, only the diffusion).         - can also be used in atmospheric set-up (for now, only the diffusion).
2016    
2017  checkpoint58x_post  checkpoint58x_post (2007/04/04)
2018  o IO option for global-file compact format:  o IO option for global-file compact format:
2019    - add options when generating topology (utils/exch2/matlab-topology-generator)    - add options when generating topology (utils/exch2/matlab-topology-generator)
2020    - add I/O capability (pkg/mdsio).    - add I/O capability (pkg/mdsio).
# Line 795  o IO option for global-file compact form Line 2022  o IO option for global-file compact form
2022    for now long-line format not yet supported by pkg/mdsio (& exch2).    for now long-line format not yet supported by pkg/mdsio (& exch2).
2023  o shelfice: add a few diagnostics  o shelfice: add a few diagnostics
2024    
2025  checkpoint58w_post  checkpoint58w_post (2007/03/13)
2026  o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:  o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
2027    rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref    rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
2028    (and replace horiVertRatio in NH code).    (and replace horiVertRatio in NH code).
# Line 816  o cpl_aim+ocn exp.: use consistent rhoCo Line 2043  o cpl_aim+ocn exp.: use consistent rhoCo
2043  o move call to cal_readparms up to make calendar parameters/variable available  o move call to cal_readparms up to make calendar parameters/variable available
2044    to all packages    to all packages
2045    
2046  checkpoint58v_post  checkpoint58v_post (2007/02/08)
2047  o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get  o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
2048    useDynP_inEos_Zc tested.    useDynP_inEos_Zc tested.
2049  o pkg/exf: changes to properly interpolate/mask/scale initial fields  o pkg/exf: changes to properly interpolate/mask/scale initial fields
# Line 835  o 2nd-Order Moment Advection Scheme (Pra Line 2062  o 2nd-Order Moment Advection Scheme (Pra
2062   - use this scheme for temperature & salinity in 2 advection test exp.:   - use this scheme for temperature & salinity in 2 advection test exp.:
2063     advect_xy & advect_xz, respectively.     advect_xy & advect_xz, respectively.
2064    
2065  checkpoint58u_post  checkpoint58u_post (2007/01/12)
2066  o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.  o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
2067  o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.  o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
2068  o testreport: add option "-skipdir" to skip some test.  o testreport: add option "-skipdir" to skip some test.
# Line 850  o add option (linFSConserveTr) to correc Line 2077  o add option (linFSConserveTr) to correc
2077  o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine  o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
2078  o pkg/thsice: fix reading mnc-pickups  o pkg/thsice: fix reading mnc-pickups
2079    
2080  checkpoint58t_post  checkpoint58t_post (2006/12/30)
2081  o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)  o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
2082  o pkg/mdsio:  o pkg/mdsio:
2083   - clean-up mdsio_readfield.F & mdsio_writefield_new.F and   - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
# Line 893  o pkg/seaice: overhaul of thermodynamics Line 2120  o pkg/seaice: overhaul of thermodynamics
2120   - introduce a few local fields to avoid modifying external fields such   - introduce a few local fields to avoid modifying external fields such
2121     as atemp, etc.     as atemp, etc.
2122    
2123  checkpoint58s_post  checkpoint58s_post (2006/12/11)
2124  o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F  o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
2125    changed exf_set_gen.F so that    changed exf_set_gen.F so that
2126      genperiod=0 means input file is one time-constant field and      genperiod=0 means input file is one time-constant field and
# Line 927  o modifications to pkg/seaice/growth.F a Line 2154  o modifications to pkg/seaice/growth.F a
2154    as actual snow thickness.  It now refers everywhere to effective snow    as actual snow thickness.  It now refers everywhere to effective snow
2155    thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.    thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
2156    
2157  checkpoint58r_post  checkpoint58r_post (2006/11/17)
2158  o modifications to pkg/seaice/growth.F, which change results of  o modifications to pkg/seaice/growth.F, which change results of
2159    lab_sea experiment: fixes pertain to melting snow over open water, to    lab_sea experiment: fixes pertain to melting snow over open water, to
2160    masking EVAP under sea ice, and to using the correct AREA variable for    masking EVAP under sea ice, and to using the correct AREA variable for
# Line 951  o Adding some pkg/diagnostics capability Line 2178  o Adding some pkg/diagnostics capability
2178  o ctrl: adding new control variables:  o ctrl: adding new control variables:
2179    lwflux, lwdown, evap, snowprecip, apressure, runoff    lwflux, lwdown, evap, snowprecip, apressure, runoff
2180    
2181  checkpoint58q_post  checkpoint58q_post (2006/10/20)
2182  o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up  o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
2183    1/6-deg Southern Ocean configuration by 8% on IBM Datastar and    1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
2184    high_res_cube configuration by 4% on Columbia.    high_res_cube configuration by 4% on Columbia.
# Line 962  o new function "MASTER_CPU_IO" (=T if ma Line 2189  o new function "MASTER_CPU_IO" (=T if ma
2189    single CPU io) so that TAF does not have to see EESUPPORT.h    single CPU io) so that TAF does not have to see EESUPPORT.h
2190  o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)  o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
2191    
2192  checkpoint58p_post  checkpoint58p_post (2006/09/08)
2193  o obcs: stop if obcs is used with useCDscheme = .true.  o obcs: stop if obcs is used with useCDscheme = .true.
2194  o shelfice:  o shelfice:
2195   - fix a sign error so that no slip at shelfice interface works   - fix a sign error so that no slip at shelfice interface works
# Line 973  o diagnoctics: modify UVELPHI and VVELPH Line 2200  o diagnoctics: modify UVELPHI and VVELPH
2200  o added adjoint exch routined for all exch*3d* routines  o added adjoint exch routined for all exch*3d* routines
2201    and updated flow directives    and updated flow directives
2202    
2203  checkpoint58o_post  checkpoint58o_post (2006/08/28)
2204  o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;  o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
2205    remove old subroutines (_XY_ & _XYZ_); update the adjoint version.    remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
2206  o change controling S/R for writing pickup file (new S/R do_write_pickup)  o change controling S/R for writing pickup file (new S/R do_write_pickup)
# Line 987  o shelfice: Line 2214  o shelfice:
2214   - add a simple boundary layer scheme to reduce noise   - add a simple boundary layer scheme to reduce noise
2215   - fix the indexing in shelfice_u/v_drag so that there will be actually drag   - fix the indexing in shelfice_u/v_drag so that there will be actually drag
2216    
2217  checkpoint58n_post  checkpoint58n_post (2006/08/14)
2218  o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to  o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
2219     local variable (not in common block).     local variable (not in common block).
2220  o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.  o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
# Line 1008  o change default MAX_NO_THREADS from 32 Line 2235  o change default MAX_NO_THREADS from 32
2235    and stop cleanly when MAX_NO_THREADS is too small.    and stop cleanly when MAX_NO_THREADS is too small.
2236  o add S/R BAR_CHECK to check multi-threaded barrier synchronization  o add S/R BAR_CHECK to check multi-threaded barrier synchronization
2237    
2238  checkpoint58m_post  checkpoint58m_post (2006/07/17)
2239  o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.  o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
2240     and side-drag) on CS-grid : global_ocean.cs32x15.viscA4     and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
2241  o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.  o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
# Line 1034  o calc_gw: true flux-form, account for h Line 2261  o calc_gw: true flux-form, account for h
2261    update rotating_tank results, but not plume_on_slope (affected at    update rotating_tank results, but not plume_on_slope (affected at
2262    truncation level, 11 digits).    truncation level, 11 digits).
2263    
2264  checkpoint58l_post  checkpoint58l_post (2006/07/12)
2265  o calc_gw:  o calc_gw:
2266   - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V   - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
2267   - remove side-drag for now (need to fix it); update plume_on_slope results.   - remove side-drag for now (need to fix it); update plume_on_slope results.
# Line 1052  o pkg/ecco: Line 2279  o pkg/ecco:
2279  o pkg/rbcs  o pkg/rbcs
2280    * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing    * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
2281    
2282  checkpoint58k_post  checkpoint58k_post (2006/07/06)
2283  o testreport:  o testreport:
2284   - always build in dir. "build" (if not there, mkdir build instead of building   - always build in dir. "build" (if not there, mkdir build instead of building
2285     & running in input)     & running in input)
# Line 1085  o tracer advection: Line 2312  o tracer advection:
2312     advection subroutine (but still not used within DST advection S/R)     advection subroutine (but still not used within DST advection S/R)
2313  o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)  o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
2314    
2315  checkpoint58j_post  checkpoint58j_post (2006/06/15)
2316  o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields  o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
2317    from file (collects calls previously in FORWARD_STEP)    from file (collects calls previously in FORWARD_STEP)
2318  o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS  o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
# Line 1093  o adjoint store dir. adjusted accordingl Line 2320  o adjoint store dir. adjusted accordingl
2320  o genmake2  o genmake2
2321    replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.    replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
2322    
2323  checkpoint58i_post  checkpoint58i_post (2006/06/14)
2324  o pkg/seaice: add parameter that allows to scale/turn off effect of seaice  o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
2325    on wind stress (SEAICEstressFactor defaults to 1.)    on wind stress (SEAICEstressFactor defaults to 1.)
2326  o Total number of Timers is finite (<=40): comment out 2 non-essential one  o Total number of Timers is finite (<=40): comment out 2 non-essential one
# Line 1107  o pkg/seaice: added SEAICEuseEVPpickup p Line 2334  o pkg/seaice: added SEAICEuseEVPpickup p
2334      non-EVP pickup files when using SEAICEuseEVP      non-EVP pickup files when using SEAICEuseEVP
2335    - fix sign error in diffusion in seaice_calc_rhs    - fix sign error in diffusion in seaice_calc_rhs
2336    
2337  checkpoint58h_post  checkpoint58h_post (2006/06/07)
2338  * Modifications for bottom topography control  * Modifications for bottom topography control
2339    o replace hFacC by _hFacC at various places    o replace hFacC by _hFacC at various places
2340    o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL    o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
# Line 1117  checkpoint58h_post Line 2344  checkpoint58h_post
2344    o works for 5x5 box, doesnt work for global_ocean.90x40x15    o works for 5x5 box, doesnt work for global_ocean.90x40x15
2345  * Adding verification for 5x5 box (4-layer) bottom topography control  * Adding verification for 5x5 box (4-layer) bottom topography control
2346    
2347  checkpoint58g_post  checkpoint58g_post (2006/06/07)
2348  o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,  o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
2349     used for mean seasonal cycle, mean diurnal cycle); add an example     used for mean seasonal cycle, mean diurnal cycle); add an example
2350     in verification/global_ocean.cs32x15/input.thsice/data.diagnostics     in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
# Line 1133  o couple pkg/thsice to pkg/seaice: Line 2360  o couple pkg/thsice to pkg/seaice:
2360  o pkg/seaice  o pkg/seaice
2361    - make (default) second order advection a bit less confusing?    - make (default) second order advection a bit less confusing?
2362    
2363  checkpoint58f_post  checkpoint58f_post (2006/06/05)
2364  o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice  o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
2365    to pkg/seaice):    to pkg/seaice):
2366    - new routines thsice_map_exf and thsice_get_exf provide the interface    - new routines thsice_map_exf and thsice_get_exf provide the interface
# Line 1164  o fix bug in aim+thsice albedo: snow & i Line 2391  o fix bug in aim+thsice albedo: snow & i
2391  o results_ad : rename "output.txt_adm" to "output_adm.txt" and change  o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
2392    testreport accordingly    testreport accordingly
2393    
2394  checkpoint58e_post  checkpoint58e_post (2006/05/17)
2395  o SEAICE_CGRID adjoint done  o SEAICE_CGRID adjoint done
2396  o R_STAR adjoint implemented.  o R_STAR adjoint implemented.
2397    * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )    * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
# Line 1172  o R_STAR adjoint implemented. Line 2399  o R_STAR adjoint implemented.
2399  o Make pkg/profile fully independent of ecco,cost, etc. stuff  o Make pkg/profile fully independent of ecco,cost, etc. stuff
2400    to be able to use it in pure forward.    to be able to use it in pure forward.
2401    
2402  checkpoint58d_post  checkpoint58d_post (2006/04/21)
2403  o upgrade simple test-experiment to tutorial example:  o upgrade simple test-experiment to tutorial example:
2404   step.1: duplicate the experiment and (step.2) will remove the old copy.   step.1: duplicate the experiment and (step.2) will remove the old copy.
2405    tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)    tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
# Line 1212  o new package prifiles: Line 2439  o new package prifiles:
2439  o Benign bug fix in initialization (spotted by M. Mazloff) of  o Benign bug fix in initialization (spotted by M. Mazloff) of
2440    ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F    ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
2441    
2442  checkpoint58c_post  checkpoint58c_post (2006/03/23)
2443  o adjoint: finish NLFS adjoint and provide reference output in  o adjoint: finish NLFS adjoint and provide reference output in
2444    verification/global_ocean.90x40x15/results_ad_nlfs    verification/global_ocean.90x40x15/results_ad_nlfs
2445  o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the  o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
# Line 1246  o seaice: Line 2473  o seaice:
2473     + move computation of the viscosities eta and zeta into a new separate     + move computation of the viscosities eta and zeta into a new separate
2474       routine (because I need to recompute them in seaice_ocean_stress.F)       routine (because I need to recompute them in seaice_ocean_stress.F)
2475    
2476  checkpoint58b_post  checkpoint58b_post (2006/03/13)
2477  o AIM+thSIce: fix sign of Short-Wave through the Ice ;  o AIM+thSIce: fix sign of Short-Wave through the Ice ;
2478    update output.txt of exp. aim.5l_cs.thSI    update output.txt of exp. aim.5l_cs.thSI
2479  o various mnc cleanups and improvements:  o various mnc cleanups and improvements:
# Line 1309  o seaice: Line 2536  o seaice:
2536      (turn on with SEAICEuseFluxForm)      (turn on with SEAICEuseFluxForm)
2537    - replace 1 in 3d global fields by kSurface in growth.F    - replace 1 in 3d global fields by kSurface in growth.F
2538        
2539  checkpoint58a_post  checkpoint58a_post (2006/02/13)
2540  o seaice:  o seaice:
2541    - bug fix in advect.F    - bug fix in advect.F
2542  o shelfice:  o shelfice:
# Line 1362  o pkg/bulk_force: Line 2589  o pkg/bulk_force:
2589     and parameters (note: calcWindStress replaces .NOT.readwindstress).     and parameters (note: calcWindStress replaces .NOT.readwindstress).
2590   - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).   - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
2591    
2592  checkpoint58  checkpoint58 (2006/01/12)
2593  o add "--embed-source" option to genmake2 which, when the supporting  o add "--embed-source" option to genmake2 which, when the supporting
2594    tools can be compiled (as determined by genmake2) will turn on the    tools can be compiled (as determined by genmake2) will turn on the
2595    embed_files package which then embeds the entire MITgcm source code    embed_files package which then embeds the entire MITgcm source code
# Line 1375  o clean up 3-dim. relaxation codes: Line 2602  o clean up 3-dim. relaxation codes:
2602    * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)    * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
2603    * Thanks to Tom Haine for testing!    * Thanks to Tom Haine for testing!
2604    
2605  checkpoint57z_post  checkpoint57z_post (2005/12/31)
2606  o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):  o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
2607    affects output (@ truncation level) of exp. plume_on_slope ; updated.    affects output (@ truncation level) of exp. plume_on_slope ; updated.
2608  o fix the pickup behavior for obcs in combination with ptracers  o fix the pickup behavior for obcs in combination with ptracers
# Line 1406  o Adding Laplacian-type smoothness const Line 2633  o Adding Laplacian-type smoothness const
2633    * Absolute scale somewhat unclear so far    * Absolute scale somewhat unclear so far
2634    * no area weighting was included since no other cost term does so far    * no area weighting was included since no other cost term does so far
2635    
2636  checkpoint57y_post  checkpoint57y_post (2005/12/08)
2637  First step for a NLFS adjoint  First step for a NLFS adjoint
2638  o initially suppress rStar (new flag DISABLE_RSTAR_CODE)  o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
2639  o new init. routines for calc_r_star, calc_surf_dr  o new init. routines for calc_r_star, calc_surf_dr
2640  o still need to deal with ini_masks_etc  o still need to deal with ini_masks_etc
2641  o testreport seemed happy  o testreport seemed happy
2642  checkpoint57y_pre  checkpoint57y_pre (2005/12/08)
2643    
2644  o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.  o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
2645  o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)  o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
# Line 1421  o cfc fixes for final year of integratio Line 2648  o cfc fixes for final year of integratio
2648  o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should  o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
2649    be in GCHEM_OPTIONS).    be in GCHEM_OPTIONS).
2650    
2651  checkpoint57x_post  checkpoint57x_post (2005/12/04)
2652  o fix testreport Pb in multiple test experiment.  o fix testreport Pb in multiple test experiment.
2653  o cleanup our namelist syntax in verification:  o cleanup our namelist syntax in verification:
2654    - make it more F95 standards compliant (some work still needed)    - make it more F95 standards compliant (some work still needed)
# Line 1441  o adjoint Line 2668  o adjoint
2668      (there are a number of extensive recomputations)      (there are a number of extensive recomputations)
2669    * Initialize certain variables needed for adjoint    * Initialize certain variables needed for adjoint
2670    
2671  checkpoint57w_post  checkpoint57w_post (2005/11/03)
2672  o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names  o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
2673               fix the singleCpuIO RS version of MDSWRITEFIELD               fix the singleCpuIO RS version of MDSWRITEFIELD
2674     and add a WARNING if using globalFiles=T with multi-processors.     and add a WARNING if using globalFiles=T with multi-processors.
# Line 1458  o PTRACERS: added namelist parameter PTR Line 2685  o PTRACERS: added namelist parameter PTR
2685    ptracers in a large domain with a constant non-zero value. Also,    ptracers in a large domain with a constant non-zero value. Also,
2686    untangle ptracers_init.F a little.    untangle ptracers_init.F a little.
2687    
2688  checkpoint57v_post  checkpoint57v_post (2005/10/13)
2689  o change dome exp. to use variable viscosity in side-drag terms.  o change dome exp. to use variable viscosity in side-drag terms.
2690  o remove all the files from the cfc_offline test since they are now  o remove all the files from the cfc_offline test since they are now
2691    incorporated into tutorial_cfc_offline which has been producing    incorporated into tutorial_cfc_offline which has been producing
# Line 1499  o reduce number of exch calls in shap_fi Line 2726  o reduce number of exch calls in shap_fi
2726  o CS-grid: fix divergence contribution to Leith viscosity. Affects (@  o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
2727    truncation level) 4/5 MLAdjust test results (11&12 digits match).    truncation level) 4/5 MLAdjust test results (11&12 digits match).
2728    
2729  checkpoint57t_post  checkpoint57t_post (2005/10/03)
2730  o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4  o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
2731  o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get  o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
2732    same truncation, independent of the face number: affects affects several    same truncation, independent of the face number: affects affects several
# Line 1522  o Clean, new version of mom_calc_visc. Line 2749  o Clean, new version of mom_calc_visc.
2749    Suggested values of viscosity parameters found in mom_calc_visc.    Suggested values of viscosity parameters found in mom_calc_visc.
2750    Many new viscosity diagnostics available.    Many new viscosity diagnostics available.
2751    
2752  checkpoint57s_post  checkpoint57s_post (2005/09/20)
2753  o Add clearing-house for viscosity calculations, mom_calc_visc and  o Add clearing-house for viscosity calculations, mom_calc_visc and
2754    correct numerous bugs in LeithD and Smagorinsky discretizations.      correct numerous bugs in LeithD and Smagorinsky discretizations.  
2755    mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be    mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
# Line 1548  o various changes to mnc including: Line 2775  o various changes to mnc including:
2775        and works with both EXCH1 and EXCH2 (but needs more testing)        and works with both EXCH1 and EXCH2 (but needs more testing)
2776    - writing works for all verification test cases w/ g77 on Linux    - writing works for all verification test cases w/ g77 on Linux
2777    
2778  checkpoint57r_post  checkpoint57r_post (2005/09/07)
2779  o make MNC variable initialization happen earlier  o make MNC variable initialization happen earlier
2780  o add diagnostics for (almost) each term of the momentum Eq.  o add diagnostics for (almost) each term of the momentum Eq.
2781  o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.  o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
# Line 1568  o new infrastructure for seaice model vs Line 2795  o new infrastructure for seaice model vs
2795  o natl_box_adjoint input_seaice for Lab. Sea now available online via wget  o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
2796    (see README file)    (see README file)
2797    
2798  checkpoint57q_post  checkpoint57q_post (2005/08/19)
2799  o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)  o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
2800  o fix annoying months-old bug in mnc/mdsio output for seaice pkg  o fix annoying months-old bug in mnc/mdsio output for seaice pkg
2801    - bug was reported by Jean-Michel and Ian Fenty    - bug was reported by Jean-Michel and Ian Fenty
# Line 1585  o Modifications to enable scripted COMMO Line 2812  o Modifications to enable scripted COMMO
2812    * verification/OpenAD/code/ has necessary scripts and description;    * verification/OpenAD/code/ has necessary scripts and description;
2813    * converts, compiles and runs successfully;    * converts, compiles and runs successfully;
2814    
2815  checkpoint57p_post  checkpoint57p_post (2005/08/01)
2816  o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F  o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
2817  o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED  o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
2818    (already the case for some pkgs, including recent MNC_init, e.g. thsice)    (already the case for some pkgs, including recent MNC_init, e.g. thsice)
# Line 1599  o Dissipation & phiHyd gradient are alwa Line 2826  o Dissipation & phiHyd gradient are alwa
2826    global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),    global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
2827    matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).    matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
2828    
2829  checkpoint57o_post  checkpoint57o_post (2005/07/30)
2830  o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and  o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
2831    (2) its ready to be documented during the 20050801 DocFest    (2) its ready to be documented during the 20050801 DocFest
2832  o MNC-ify the gmredi package -- tested and works w/ and w/o mnc  o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
# Line 1608  o set to #undef CTRL_SET_OLD_MAXCVARS_30 Line 2835  o set to #undef CTRL_SET_OLD_MAXCVARS_30
2835    in global1x1_tot/code_seaice_adj to access indices 32, 33    in global1x1_tot/code_seaice_adj to access indices 32, 33
2836    (worth another tag)    (worth another tag)
2837    
2838  checkpoint57n_post  checkpoint57n_post (2005/07/29)
2839  o adding precip control xx_precip 32  o adding precip control xx_precip 32
2840  o adding swflux control xx_swflux 33  o adding swflux control xx_swflux 33
2841  o Replacing 10 forcing penalty cost routines by 1 generic.  o Replacing 10 forcing penalty cost routines by 1 generic.
# Line 1624  o enable useSingleCpuIO for mdsio vector Line 2851  o enable useSingleCpuIO for mdsio vector
2851    (applies in particular to tapelev I/O)    (applies in particular to tapelev I/O)
2852  o removed inefficient K-loop in all active_file*control*.F  o removed inefficient K-loop in all active_file*control*.F
2853    
2854  checkpoint57m_post  checkpoint57m_post (2005/07/28)
2855  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
2856    and advect_cs (use EXCH-2 and standard cs-32 grid files).    and advect_cs (use EXCH-2 and standard cs-32 grid files).
2857  o pkg/exch2: filling of face-corner halo regions is optional  o pkg/exch2: filling of face-corner halo regions is optional
2858    (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.    (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
2859    
2860  checkpoint57l_post  checkpoint57l_post (2005/07/14)
2861   tag before updating tutorials (pre-release-2)   tag before updating tutorials (pre-release-2)
2862  o add cos & sin of grid-direction orientation angle (curvilinear grid only,  o add cos & sin of grid-direction orientation angle (curvilinear grid only,
2863     for output and interpolation of input fields onto model grid)     for output and interpolation of input fields onto model grid)
# Line 1642  o fix aim_diagnostics_init.F mate number Line 2869  o fix aim_diagnostics_init.F mate number
2869  o add mnc output capability to diagnostics/diagstat and update  o add mnc output capability to diagnostics/diagstat and update
2870    our cvsignore files for the ACSII output generated    our cvsignore files for the ACSII output generated
2871    
2872  checkpoint57k_post  checkpoint57k_post (2005/07/02)
2873  o lab_sea now uses diagnostics package and provides a suite of  o lab_sea now uses diagnostics package and provides a suite of
2874    new EXF diagnostics output.    new EXF diagnostics output.
2875    
2876  checkpoint57j_post  checkpoint57j_post (2005/06/30)
2877  o exf  o exf
2878    * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):    * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
2879      Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);      Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
# Line 1676  o fix bug in rStar code (calc_r_star.F) Line 2903  o fix bug in rStar code (calc_r_star.F)
2903  o fix few little things to avoid floating error with -ftrapuv (ifort v9)  o fix few little things to avoid floating error with -ftrapuv (ifort v9)
2904   (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)   (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
2905    
2906  checkpoint57i_post  checkpoint57i_post (2005/06/19)
2907  o Diagnostics package was changed: diagnostic allocation is now deactivated  o Diagnostics package was changed: diagnostic allocation is now deactivated
2908    by setting an empty file name in the namelist (used to be by setting 0 frequency)    by setting an empty file name in the namelist (used to be by setting 0 frequency)
2909  o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;  o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
# Line 1695  o pkg/diagnostics: Line 2922  o pkg/diagnostics:
2922    tested against monitor output (including land & thSIce) on various exp.    tested against monitor output (including land & thSIce) on various exp.
2923  o make seaice-pkg I/O type flags (MNC/MDS) more standard.  o make seaice-pkg I/O type flags (MNC/MDS) more standard.
2924    
2925  checkpoint57h_done  checkpoint57h_done (2005/05/19)
2926    tag after changing user customized files (DIAGNOSTICS_SIZE.h,    tag after changing user customized files (DIAGNOSTICS_SIZE.h,
2927    data.diagnostics, data.gchem, data.ptracers) is done.    data.diagnostics, data.gchem, data.ptracers) is done.
2928    
# Line 1704  o pkg/diagnostics: prepare for Global/Re Line 2931  o pkg/diagnostics: prepare for Global/Re
2931  o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE  o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
2932    and rename it: DIFFERENT_MULTIPLE    and rename it: DIFFERENT_MULTIPLE
2933    
2934  checkpoint57h_post  checkpoint57h_post (2005/05/14)
2935  o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers  o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
2936  o pkg/diagnostics: change output frequency, now in seconds (instead  o pkg/diagnostics: change output frequency, now in seconds (instead
2937    of Nb of iterations). This requires to change data.diagnostics.    of Nb of iterations). This requires to change data.diagnostics.
2938  checkpoint57h_pre  checkpoint57h_pre (2005/05/12)
2939    
2940  o in mnc, let the user create the output dir if both mnc_outdir_date  o in mnc, let the user create the output dir if both mnc_outdir_date
2941    and mnc_outdir_num are false    and mnc_outdir_num are false
# Line 1722  o test AB-3 code with 4th.Order advectio Line 2949  o test AB-3 code with 4th.Order advectio
2949  o fix mnc flags in pkg/seaice so that they are "owned" by seaice,  o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
2950    not mnc -- this mistake was found by JMC and is now corrected    not mnc -- this mistake was found by JMC and is now corrected
2951    
2952  checkpoint57g_post  checkpoint57g_post (2005/04/15)
2953  o add Adams-Bashforth 3rd Order time stepping:  o add Adams-Bashforth 3rd Order time stepping:
2954    - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)    - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
2955    - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...    - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
2956  checkpoint57g_pre  checkpoint57g_pre (2005/04/15)
2957    
2958  o make lambda[Theta,Salt]ClimRelax spatially varying  o make lambda[Theta,Salt]ClimRelax spatially varying
2959    (default remains spatially uniform constant based on tau)    (default remains spatially uniform constant based on tau)
# Line 1736  o added new control variables Line 2963  o added new control variables
2963  o separate masks used for ctrl_pack/unpack 'from write_grid' output  o separate masks used for ctrl_pack/unpack 'from write_grid' output
2964    (suggested by G. Forget)    (suggested by G. Forget)
2965    
2966  checkpoint57f_post  checkpoint57f_post (2005/04/06)
2967  o add parameter "baseTime" = model base time = time at iteration zero  o add parameter "baseTime" = model base time = time at iteration zero
2968    new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to    new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
2969    account for baseTime shift    account for baseTime shift
2970  o move Coriolis arrays from PARAMS.h to GRID.h  o move Coriolis arrays from PARAMS.h to GRID.h
2971  checkpoint57f_pre  checkpoint57f_pre (2005/04/06)
2972    
2973  o mnc-ifying the seaice package  o mnc-ifying the seaice package
2974  o introduced an alternative length scale calculation for use in the limiting  o introduced an alternative length scale calculation for use in the limiting
# Line 1762  o adjoint-related modifications Line 2989  o adjoint-related modifications
2989    * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33    * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
2990    * mom_vi_hdissip: to be able to use Leith scheme in adjoint    * mom_vi_hdissip: to be able to use Leith scheme in adjoint
2991    
2992  checkpoint57e_post  checkpoint57e_post (2005/02/28)
2993  o Adding eddy stress controls a la Ferreira et al.  o Adding eddy stress controls a la Ferreira et al.
2994  checkpoint57e_pre (actually was tagged: eckpoint57e_pre)  checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
2995    
# Line 1780  o diagnostics: add pickup functionality Line 3007  o diagnostics: add pickup functionality
3007  o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.  o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
3008  o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)  o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
3009    
3010  checkpoint57d_post  checkpoint57d_post (2005/02/11)
3011  o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing  o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
3012  o modify verification/ideal_2D_oce so that it tests the creation of mnc  o modify verification/ideal_2D_oce so that it tests the creation of mnc
3013    output from the diagnostics package    output from the diagnostics package
# Line 1802  o move state variable diagnostics to the Line 3029  o move state variable diagnostics to the
3029    (note: still needs some work specially for snap-shot diagnostics)    (note: still needs some work specially for snap-shot diagnostics)
3030    duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z    duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
3031    
3032  checkpoint57c_post  checkpoint57c_post (2005/01/27)
3033  o Change testing option (-ieee) to get closer agreement between g77 & ifort  o Change testing option (-ieee) to get closer agreement between g77 & ifort
3034  o generate new output.txt files on faulks with g77 & the new -ieee option  o generate new output.txt files on faulks with g77 & the new -ieee option
3035  checkpoint57c_pre  checkpoint57c_pre (2005/01/27)
3036    
3037  o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);  o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
3038    update output.txt of exp. global_ocean.90x40x15    update output.txt of exp. global_ocean.90x40x15
# Line 1838  o pkg/mdsio/ Line 3065  o pkg/mdsio/
3065    * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F    * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
3066    * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)    * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
3067    
3068  checkpoint57b_post  checkpoint57b_post (2004/12/20)
3069  o simplify options in diagnostics_fill arguments (remove weird combinations)  o simplify options in diagnostics_fill arguments (remove weird combinations)
3070  o fix MNC coordinate variables so that they now contain per-face index  o fix MNC coordinate variables so that they now contain per-face index
3071    values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in    values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
# Line 1884  o re-arrange diagnostics pkg initialisat Line 3111  o re-arrange diagnostics pkg initialisat
3111     look through the short list of active diag. (instead of the long list)     look through the short list of active diag. (instead of the long list)
3112     create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active     create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
3113    
3114  checkpoint57a_post  checkpoint57a_post (2004/12/10)
3115  o this set of changes restores TAMC compatibility  o this set of changes restores TAMC compatibility
3116    tested for global_ocean.90x40x15 adjoint on trough    tested for global_ocean.90x40x15 adjoint on trough
3117    (what a pain)    (what a pain)
3118    
3119  checkpoint57a_pre  checkpoint57a_pre (2004/12/10)
3120  o some modifs in tools/build_options for sunos  o some modifs in tools/build_options for sunos
3121  o call ctrl_pack for ctrl at end for optimcycle=0  o call ctrl_pack for ctrl at end for optimcycle=0
3122    
3123  checkpoint57  checkpoint57 (2004/12/09)
3124  o add horizontal bi-harmonic viscosity for vertical velocity  o add horizontal bi-harmonic viscosity for vertical velocity
3125    - new parameter viscA4W (defaults to viscA4)    - new parameter viscA4W (defaults to viscA4)
3126    - affects only non-hydrostatic code    - affects only non-hydrostatic code
# Line 1911  o untangle a few ifdefs related to cost, Line 3138  o untangle a few ifdefs related to cost,
3138  o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)  o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
3139    (theta2, salt2 in ecco_cost_weights)    (theta2, salt2 in ecco_cost_weights)
3140    
3141  checkpoint56c_post  checkpoint56c_post (2004/12/03)
3142  o OBCS as control variables  o OBCS as control variables
3143    - update ctrl_ad_diff.list, obcs_ad_diff.list    - update ctrl_ad_diff.list, obcs_ad_diff.list
3144    - remove balance of obcs controls from default    - remove balance of obcs controls from default
# Line 1929  o exf: Line 3156  o exf:
3156  o mdsio:  o mdsio:
3157    - i/o-vector change debugLevel from debLevA to debLevB    - i/o-vector change debugLevel from debLevA to debLevB
3158    
3159  checkpoint56b_post  checkpoint56b_post (2004/12/01)
3160  o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that  o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
3161    is called from DO_THE_MODEL_IO    is called from DO_THE_MODEL_IO
3162    - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE    - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
# Line 1944  o testreport previously did a lousy job Line 3171  o testreport previously did a lousy job
3171    testreport.    testreport.
3172  o ptracers_monitor: bug fix for MPI  o ptracers_monitor: bug fix for MPI
3173    
3174  checkpoint56a_post  checkpoint56a_post (2004/11/28)
3175  o GCHEM: finish reorganizating the package  o GCHEM: finish reorganizating the package
3176    - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency    - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
3177      (introduces another 3D-array for each passive tracer, but only if      (introduces another 3D-array for each passive tracer, but only if
# Line 1989  o GCHEM: Line 3216  o GCHEM:
3216    - cleaning up    - cleaning up
3217  o small cleaning of exch2: remove files that are also in eesupp/src  o small cleaning of exch2: remove files that are also in eesupp/src
3218    
3219  checkpoint56  checkpoint56 (2004/11/17)
3220  o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0  o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
3221  o mnc: cleanup "full" files--fixes out-of-memory problem  o mnc: cleanup "full" files--fixes out-of-memory problem
3222  o ECCO-GODAE  o ECCO-GODAE
# Line 2019  o mdsio: filename info to both stderr, s Line 3246  o mdsio: filename info to both stderr, s
3246  o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]  o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
3247    from sign change    from sign change
3248    
3249  checkpoint55j_post  checkpoint55j_post (2004/11/10)
3250  o isolate dissipation tendency (allow to keep it out off AB) in V.I form.  o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
3251    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
3252  o add consistent build directories and .cvsignore files to verification  o add consistent build directories and .cvsignore files to verification
# Line 2030  o make all subroutines 30 or less charac Line 3257  o make all subroutines 30 or less charac
3257  o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;  o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
3258    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
3259    
3260  checkpoint55i_post  checkpoint55i_post (2004/10/28)
3261  o change arrays for total vertical diffusivity (2.D if explicit,  o change arrays for total vertical diffusivity (2.D if explicit,
3262    3.D if implicit) ; each ptracer uses its own background value.    3.D if implicit) ; each ptracer uses its own background value.
3263  o added mnc/NetCDF output capability to ocn_compon_interf  o added mnc/NetCDF output capability to ocn_compon_interf
# Line 2045  o give MNC the ability to create additio Line 3272  o give MNC the ability to create additio
3272  o Compute the non-local term using either KPP vertical diffusivity (=default)  o Compute the non-local term using either KPP vertical diffusivity (=default)
3273     or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)     or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
3274    
3275  checkpoint55h_post  checkpoint55h_post (2004/10/20)
3276  o add verification test "vermix"  o add verification test "vermix"
3277  o remove all the *_ioinc flags and replace with the single global  o remove all the *_ioinc flags and replace with the single global
3278    outputTypesInclusive flag    outputTypesInclusive flag
# Line 2053  o allow to set a vertical profile of ver Line 3280  o allow to set a vertical profile of ver
3280  o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS  o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
3281  o useMNC moved from data.mnc to data.pkg  o useMNC moved from data.mnc to data.pkg
3282    
3283  checkpoint55g_post  checkpoint55g_post (2004/10/14)
3284  o Renaming carbon AD experiments to comply with testreport conventions  o Renaming carbon AD experiments to comply with testreport conventions
3285  o Updating adjoint of Held-Suarez hs94.1x64x5  o Updating adjoint of Held-Suarez hs94.1x64x5
3286  o Fixing directives for non-ECCO forward_step, after ECCO directives  o Fixing directives for non-ECCO forward_step, after ECCO directives
# Line 2063  o Fixing directives for non-ECCO forward Line 3290  o Fixing directives for non-ECCO forward
3290  o Updating adjoint output for natl_box_adjoint after  o Updating adjoint output for natl_box_adjoint after
3291    pkg/ecco has been modified (see taga c55d_post)    pkg/ecco has been modified (see taga c55d_post)
3292    
3293  checkpoint55f_post  checkpoint55f_post (2004/10/13)
3294  o rename to timeave_init_fixed  o rename to timeave_init_fixed
3295    
3296  checkpoint55e_post  checkpoint55e_post (2004/10/13)
3297  o some delicate re-shuffle of store directives to avoid one  o some delicate re-shuffle of store directives to avoid one
3298    extra call of do_oceanic_physics    extra call of do_oceanic_physics
3299    affects ecco_the_main_loop.F, do_oceanic_physics.F    affects ecco_the_main_loop.F, do_oceanic_physics.F
# Line 2074  o some delicate re-shuffle of store dire Line 3301  o some delicate re-shuffle of store dire
3301  o NB: this may break global_ocean adjoint temporarily,  o NB: this may break global_ocean adjoint temporarily,
3302    but it is clear how to fix it. Will do later, need this now.    but it is clear how to fix it. Will do later, need this now.
3303    
3304  checkpoint55d_post  checkpoint55d_post (2004/10/11)
3305  o ECCO specific cost function terms (up-to-date with 1x1 runs)  o ECCO specific cost function terms (up-to-date with 1x1 runs)
3306  o ecco_cost_weights is modified to 1x1 runs  o ecco_cost_weights is modified to 1x1 runs
3307  o modifs to allow observations to be read in as  o modifs to allow observations to be read in as
3308    single file or yearly files    single file or yearly files
3309  o enable to read exf forcing fields as either  o enable to read exf forcing fields as either
3310    single file or yearly files (flag useExfYearlyFields)    single file or yearly files (flag useExfYearlyFields)
3311  checkpoint55d_pre  checkpoint55d_pre (2004/10/08)
3312    
3313  o switch between 2-level and 3-level checkpointing  o switch between 2-level and 3-level checkpointing
3314  o add ability of MNC to write local and "partial" (eg. 2D slices where  o add ability of MNC to write local and "partial" (eg. 2D slices where
# Line 2129  o more obcs stuff Line 3356  o more obcs stuff
3356    - changed argument list of OBCS_CALC to myTime+deltaTclock    - changed argument list of OBCS_CALC to myTime+deltaTclock
3357    - fixed about 35 bugs in obcs_external_fields_load    - fixed about 35 bugs in obcs_external_fields_load
3358    
3359  checkpoint55c_post  checkpoint55c_post (2004/09/23)
3360  o obcs stuff  o obcs stuff
3361    - new runtime flags useOBCSprescribe, useOBCSbalance    - new runtime flags useOBCSprescribe, useOBCSbalance
3362    - re-arranged obcs_calc    - re-arranged obcs_calc
# Line 2143  o obcs stuff Line 3370  o obcs stuff
3370  o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments  o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
3371    which simplifies the calls and passes the ifc check-bounds test    which simplifies the calls and passes the ifc check-bounds test
3372    
3373  checkpoint55b_post  checkpoint55b_post (2004/09/22)
3374  o add a 2D scalar, Z location, exchange_2 routine.  o add a 2D scalar, Z location, exchange_2 routine.
3375  o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows  o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
3376    to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]    to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
# Line 2154  o use a more standard discretization for Line 3381  o use a more standard discretization for
3381  o fix gad_advection.F (CubedSphere part), back to version 1.23  o fix gad_advection.F (CubedSphere part), back to version 1.23
3382  o fix bug in mom_vi_del2uv.F (CubedSphere part).  o fix bug in mom_vi_del2uv.F (CubedSphere part).
3383    
3384  checkpoint55a_post  checkpoint55a_post (2004/09/20)
3385  o merged code to  o merged code to
3386    * prescribe/read time-dependent open boundaries    * prescribe/read time-dependent open boundaries
3387      (works in conjunction with exf, cal)      (works in conjunction with exf, cal)
# Line 2162  o merged code to Line 3389  o merged code to
3389    * each boundary N/S/E/W now has its own CPP option    * each boundary N/S/E/W now has its own CPP option
3390      (healthy for the adjoint)      (healthy for the adjoint)
3391    
3392  checkpoint55  checkpoint55 (2004/09/17)
3393  o up-to-date adjoint of previous breaks  o up-to-date adjoint of previous breaks
3394    - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix    - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
3395    - global_ocean_ebm: adjoint still needs fix (TLM ok)    - global_ocean_ebm: adjoint still needs fix (TLM ok)
# Line 2172  o up-to-date adjoint of previous breaks Line 3399  o up-to-date adjoint of previous breaks
3399  o remove all tr1-related code (ALLOW_PASSIVE_TRACER)  o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
3400    (adjoint stuff still has some tr1 'names', but all use ptracer arrays)    (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
3401    
3402  checkpoint54f_post  checkpoint54f_post (2004/09/16)
3403  o in verification/carbin/ remove experiment related to  o in verification/carbin/ remove experiment related to
3404    ALLOW_PASSIVE_TRACER (array tr1 etc)    ALLOW_PASSIVE_TRACER (array tr1 etc)
3405    code_ad/ input_ad/ results_ad    code_ad/ input_ad/ results_ad
# Line 2198  o overhaul of IO so that we now have fla Line 3425  o overhaul of IO so that we now have fla
3425    - numerous small formatting cleanups for ProTeX    - numerous small formatting cleanups for ProTeX
3426  o add version info (via BUILD_INFO.h) to MNC and stdout  o add version info (via BUILD_INFO.h) to MNC and stdout
3427    
3428  checkpoint54e_post  checkpoint54e_post (2004/09/02)
3429  o add two new packages  o add two new packages
3430    - pp81 (Packanowski and Philander, 1981), Richardson number and    - pp81 (Packanowski and Philander, 1981), Richardson number and
3431      stratification dependent mixing      stratification dependent mixing
3432    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
3433    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
3434      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
3435      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
3436  o add offline package  o add offline package
3437  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
3438    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz
3439  o genmake2: add ability to search for C compilers and cleanup test output  o genmake2: add ability to search for C compilers and cleanup test output
3440    - fixes recent SX-6 problems and should help with others (eg. HP-UX)    - fixes recent SX-6 problems and should help with others (eg. HP-UX)
3441    
3442  checkpoint54d_post  checkpoint54d_post (2004/07/27)
3443  o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed  o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
3444  o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,  o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
3445    leading to additional shift by 5 days each year of integration    leading to additional shift by 5 days each year of integration
# Line 2228  o fix a bug in Flux deriv. vs Ts (pkg/ai Line 3455  o fix a bug in Flux deriv. vs Ts (pkg/ai
3455  o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")  o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
3456  o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)  o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
3457    
3458  checkpoint54c_post  checkpoint54c_post (2004/07/18)
3459  o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr  o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
3460    this affects (truncation error) output.txt of test-exp:    this affects (truncation error) output.txt of test-exp:
3461     global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box     global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
# Line 2239  o define the max number of passive trace Line 3466  o define the max number of passive trace
3466  o start to test mnc routinely in exp0  o start to test mnc routinely in exp0
3467  o add sea-ice loading (sIceLoad) as a new forcing field.  o add sea-ice loading (sIceLoad) as a new forcing field.
3468    
3469  checkpoint54b_post  checkpoint54b_post (2004/07/08)
3470  o add testreport "-j JOBS" option for parallel builds (tested and pretty  o add testreport "-j JOBS" option for parallel builds (tested and pretty
3471     impressive on Altix and Opteron systems)     impressive on Altix and Opteron systems)
3472  o diagnostics can now write NetCDF files through the mnc package  o diagnostics can now write NetCDF files through the mnc package
# Line 2249  o staggerTimeStep & NLFS: rescale T & S Line 3476  o staggerTimeStep & NLFS: rescale T & S
3476    affects (truncation error) output of lab_sea & natl_box exp.: updated    affects (truncation error) output of lab_sea & natl_box exp.: updated
3477  o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)  o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
3478    
3479  checkpoint54a_post  checkpoint54a_post (2004/07/06)
3480  o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).  o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
3481  o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)  o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
3482  o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)  o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
3483  o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)  o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
3484    + internal_wave (shift in writing cg2d_ini_res)    + internal_wave (shift in writing cg2d_ini_res)
3485  checkpoint54a_pre  checkpoint54a_pre (2004/07/05)
3486    
3487  o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice  o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
3488    - modified verification/lab_sea and natl_box_adjoint accordingly    - modified verification/lab_sea and natl_box_adjoint accordingly
3489    
3490  checkpoint54  checkpoint54 (2004/07/02)
3491  checkpoint53g_post  checkpoint53g_post (2004/07/02)
3492  o prepare splitting of thermodynamics: store convect.counter in common block  o prepare splitting of thermodynamics: store convect.counter in common block
3493  o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)  o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
3494    output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave    output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
# Line 2270  o new parameter "nShapS": allow to treat Line 3497  o new parameter "nShapS": allow to treat
3497  o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)  o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
3498  o restore adjointability  o restore adjointability
3499    
3500  checkpoint53f_post  checkpoint53f_post (2004/06/25)
3501  o modifications that affect AIM experiment results (update output.txt):  o modifications that affect AIM experiment results (update output.txt):
3502    - no advection of S at top interface Nr (pkg/generic_advdiff)    - no advection of S at top interface Nr (pkg/generic_advdiff)
3503    - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)    - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
# Line 2283  o merged cylindrical coord configuration Line 3510  o merged cylindrical coord configuration
3510  o added rotating_tank experiment  o added rotating_tank experiment
3511  checkpoint53e_pre  checkpoint53e_pre
3512    
3513  checkpoint53d_post  checkpoint53d_post (2004/06/14)
3514  o faulks upgraded: re-generate output.txt that have changed:  o faulks upgraded: re-generate output.txt that have changed:
3515     global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box     global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
3516  o Added Bryan and Lewis, 1979, vertical diffusivity profile  o Added Bryan and Lewis, 1979, vertical diffusivity profile
# Line 2302  o regenerated output for global_ocean_eb Line 3529  o regenerated output for global_ocean_eb
3529  o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation  o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
3530    of mom_common/    of mom_common/
3531    - simple re-arrangement of instructions within computing loop    - simple re-arrangement of instructions within computing loop
3532  checkpoint53d_pre  checkpoint53d_pre (2004/05/21)
3533    
3534  checkpoint53c_post  checkpoint53c_post (2004/05/21)
3535  o new version of coupler for AIM+thSIce and Ocean models  o new version of coupler for AIM+thSIce and Ocean models
3536   - new fields (SSS,h_MixLayer ...) are exchanged through the coupler   - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
3537   - land: change Evaporation of snow   - land: change Evaporation of snow
# Line 2321  o Adjoint of EBM package + verification Line 3548  o Adjoint of EBM package + verification
3548    * TLM OK    * TLM OK
3549    * ADM not sufficient accuracy yet (needs further testing)    * ADM not sufficient accuracy yet (needs further testing)
3550    
3551  checkpoint53b_post  checkpoint53b_post (2004/05/14)
3552  o Commiting new energy balance model to repository  o Commiting new energy balance model to repository
3553    * package is pkg/ebm    * package is pkg/ebm
3554    * verif. is verification/global_ocean_ebm    * verif. is verification/global_ocean_ebm
# Line 2339  C        Destabilization of the thermoha Line 3566  C        Destabilization of the thermoha
3566  C        by atmospheric eddy transports.  C        by atmospheric eddy transports.
3567  C        J. Climate 7(12), 1870-1882  C        J. Climate 7(12), 1870-1882
3568  o Will need long integration testing.  o Will need long integration testing.
3569  checkpoint53b_pre  checkpoint53b_pre (2004/05/14)
3570    
3571  o created pkg/mom_common in preparation for variable viscosity code  o created pkg/mom_common in preparation for variable viscosity code
3572  o renamed and split ini_mnc_io  o renamed and split ini_mnc_io
# Line 2347  o pkg/land: only liquid water can diffus Line 3574  o pkg/land: only liquid water can diffus
3574  o AIM using land: soil wetness availability account for snow  o AIM using land: soil wetness availability account for snow
3575  o added printMapIncludesZeros to EEPARMS namelist  o added printMapIncludesZeros to EEPARMS namelist
3576    
3577  checkpoint53a_post  checkpoint53a_post (2004/05/11)
3578  o restore TAMC compatiility for exf_constants.h  o restore TAMC compatiility for exf_constants.h
3579    (no usage of _d in .h)    (no usage of _d in .h)
3580  o Additional storing in KPP in an attempt to fix  o Additional storing in KPP in an attempt to fix
# Line 2360  o Fixed verification/natl_box_adjoint ex Line 3587  o Fixed verification/natl_box_adjoint ex
3587    and hence gives results closer to that of Experiment 2.    and hence gives results closer to that of Experiment 2.
3588    Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.    Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
3589    
3590  checkpoint53  checkpoint53 (2004/05/06)
3591  o stable checkpoint with up to date adjoint  o stable checkpoint with up to date adjoint
3592    TLM tests only run for 1st grdchk at the moment. Its unclear if    TLM tests only run for 1st grdchk at the moment. Its unclear if
3593    this is a code problem or a problem with resetting code for g_    this is a code problem or a problem with resetting code for g_
# Line 2370  o stable checkpoint with up to date adjo Line 3597  o stable checkpoint with up to date adjo
3597     o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)     o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
3598       are both still in chaos following their security messes.       are both still in chaos following their security messes.
3599    
3600  checkpoint52n_post  checkpoint52n_post (2004/05/06)
3601  o various build (mostly genmake2) changes including:  o various build (mostly genmake2) changes including:
3602    - ability to build/run more easily within Cygwin and MacOS X    - ability to build/run more easily within Cygwin and MacOS X
3603    - more complicated Makefiles with a stronger dependence on Gnu Make    - more complicated Makefiles with a stronger dependence on Gnu Make
# Line 2401  o fix in pkg/thsice: Line 3628  o fix in pkg/thsice:
3628    - maintain snow precipitation unchanged (even if Tsf >=0).    - maintain snow precipitation unchanged (even if Tsf >=0).
3629   both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice   both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
3630    
3631  checkpoint52m_post  checkpoint52m_post (2004/04/18)
3632  o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;  o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
3633    this does not change any of the results, because myIter=0 in swfrac always    this does not change any of the results, because myIter=0 in swfrac always
3634    lead to jwtype=2 (the default anyway), but the call makes little sense    lead to jwtype=2 (the default anyway), but the call makes little sense
# Line 2433  o test exp. advect_cs: use the standard Line 3660  o test exp. advect_cs: use the standard
3660  o Added functionality to grdchk:  o Added functionality to grdchk:
3661    pick global i,j,k position (or nearest wet) where to perform check.    pick global i,j,k position (or nearest wet) where to perform check.
3662    
3663  checkpoint52l_post  checkpoint52l_post (2004/03/11)
3664  o new land formulation:  o new land formulation:
3665    a) use ground enthalpy as prognostic variable to ensure exact    a) use ground enthalpy as prognostic variable to ensure exact
3666       energy conservation.       energy conservation.
# Line 2444  o aim_v23 modification for new land mode Line 3671  o aim_v23 modification for new land mode
3671    a) Treat separately land / ocean / sea-ice surface fluxes    a) Treat separately land / ocean / sea-ice surface fluxes
3672       to allow implicit computation of land & sea-ice surface temp.       to allow implicit computation of land & sea-ice surface temp.
3673    b) add snow precipitation.    b) add snow precipitation.
3674  checkpoint52l_pre  checkpoint52l_pre (2004/03/11)
3675    
3676  o fix problem (when 1 tile is empty) in min/max monitor.  o fix problem (when 1 tile is empty) in min/max monitor.
3677  o fix bug in timeAve (u,vZetatave in common block)  o fix bug in timeAve (u,vZetatave in common block)
# Line 2457  o fix ini_curvilinear_grid ; test CS exp Line 3684  o fix ini_curvilinear_grid ; test CS exp
3684  o aim.5l_cs: modify sea-ice fraction input file ; update output  o aim.5l_cs: modify sea-ice fraction input file ; update output
3685  o exf: Adding simple range check routine for exf fields after read  o exf: Adding simple range check routine for exf fields after read
3686    
3687  checkpoint52k_post  checkpoint52k_post (2004/02/23)
3688  o removed top-level directory "diags"  o removed top-level directory "diags"
3689    - we migrated these functions to pkg/timeave a long time ago    - we migrated these functions to pkg/timeave a long time ago
3690  o fixed bug introduced in pkg/monitor  o fixed bug introduced in pkg/monitor
# Line 2470  o set all ...Freq to zero after cost_fin Line 3697  o set all ...Freq to zero after cost_fin
3697    taveFreq, dumpFreq, pChkptFreq    taveFreq, dumpFreq, pChkptFreq
3698  o MAIN and ECCO differentiability restored  o MAIN and ECCO differentiability restored
3699    
3700  checkpoint52j_post  checkpoint52j_post (2004/02/18)
3701  o fix nchklev in tamc.h for global_ocean...  o fix nchklev in tamc.h for global_ocean...
3702  o Bringing flow and store directives up-to-date  o Bringing flow and store directives up-to-date
3703  o Really weird thing!  o Really weird thing!
# Line 2478  o Really weird thing! Line 3705  o Really weird thing!
3705    starttime, niter0, instead of mytime, myiter, screws up the adjoint:    starttime, niter0, instead of mytime, myiter, screws up the adjoint:
3706    TAF places a faulty re-call of initialise_varia    TAF places a faulty re-call of initialise_varia
3707    after cost_final call which should not be there!    after cost_final call which should not be there!
3708  checkpoint52j_pre  checkpoint52j_pre (2004/02/03)
3709    
3710  o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and  o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
3711    error messages    error messages
# Line 2495  o merged mom_vi_calc_relvort3.F, mom_vi_ Line 3722  o merged mom_vi_calc_relvort3.F, mom_vi_
3722    mon_vort3.F to make exch2 friendly with >1 tile per cube face    mon_vort3.F to make exch2 friendly with >1 tile per cube face
3723  o limit timeave output for hi-res integrations  o limit timeave output for hi-res integrations
3724    
3725  checkpoint52i_post  checkpoint52i_post (2004/01/21)
3726  o removed CPP_EEOPTIONS.h from verification/*/code  o removed CPP_EEOPTIONS.h from verification/*/code
3727  o updated the tiling for global_ocean_pressure  o updated the tiling for global_ocean_pressure
3728  checkpoint52i_pre  checkpoint52i_pre (2004/01/20)
3729    
3730  o update aim.5l_LatLon using the standard aim_v23 pkg (instead of  o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
3731    the old pkg/aim).    the old pkg/aim).
3732    
3733  checkpoint52h_pre  checkpoint52h_pre (2004/01/20)
3734  o shortened offending lines in exch2_send_rx?.template  o shortened offending lines in exch2_send_rx?.template
3735  o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator  o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
3736  o genmake2: add build & execute test for NetCDF code  o genmake2: add build & execute test for NetCDF code
# Line 2514  o added temporary hack for sea-ice dynam Line 3741  o added temporary hack for sea-ice dynam
3741    metric terms are ignored and it is assumed that    metric terms are ignored and it is assumed that
3742    there is no sea-ice on cube faces 1, 2, 4, and 5.    there is no sea-ice on cube faces 1, 2, 4, and 5.
3743    
3744  checkpoint52f_post  checkpoint52f_post (2004/01/09)
3745  o added exch2 cube routines to pkg/exch2  o added exch2 cube routines to pkg/exch2
3746  o modified hs94.cs-32x32x5 to use it  o modified hs94.cs-32x32x5 to use it
3747  o added new grid files to hs94.cs-32x32x5  o added new grid files to hs94.cs-32x32x5
3748  checkpoint52f_pre  checkpoint52f_pre (2004/01/07)
3749    
3750  checkpoint52e_post  checkpoint52e_post (2004/01/07)
3751  o first attempt to solve vertical advection (momemtum & T,S) Implicitly  o first attempt to solve vertical advection (momemtum & T,S) Implicitly
3752    for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)    for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
3753  o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)  o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
# Line 2528  o step.1 : rewrite (as in MultiDimAdvec) Line 3755  o step.1 : rewrite (as in MultiDimAdvec)
3755  o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.  o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
3756  o update output (gad_calc_rhs.F changes affect truncation error) of exp:  o update output (gad_calc_rhs.F changes affect truncation error) of exp:
3757   front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box   front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
3758  checkpoint52e_pre  checkpoint52e_pre (2004/01/02)
3759    
3760  o fix bug in impldiff when Nr=1 or Nr=2.  o fix bug in impldiff when Nr=1 or Nr=2.
3761  o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt  o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
# Line 2539  o added exf_offset_atemp for Celsius to Line 3766  o added exf_offset_atemp for Celsius to
3766  o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024  o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
3767  o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations  o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
3768    
3769  checkpoint52d_post  checkpoint52d_post (2003/12/16)
3770  o re-tiled many expts to allow comparison in multi-processor mode  o re-tiled many expts to allow comparison in multi-processor mode
3771    - updated output accordingly    - updated output accordingly
3772    - changed hs94.128x64x5 to use intial T from file rather than use the    - changed hs94.128x64x5 to use intial T from file rather than use the
# Line 2568  o check-in the first version of the coup Line 3795  o check-in the first version of the coup
3795  o new verification experiment, cpl_aim+ocn:  o new verification experiment, cpl_aim+ocn:
3796     coupled ocean - AIM atmosphere on cs32 grid.     coupled ocean - AIM atmosphere on cs32 grid.
3797    
3798  checkpoint52d_pre  checkpoint52d_pre (2003/12/06)
3799  o surface flux time-av diagnostic modified for NLFS & RealFreshWater  o surface flux time-av diagnostic modified for NLFS & RealFreshWater
3800  o add call to AIM pendant S/R in external_forcing & external_fields_load.F  o add call to AIM pendant S/R in external_forcing & external_fields_load.F
3801    
3802  checkpoint52c_post  checkpoint52c_post (2003/11/25)
3803  o Fixing OPTIONS files for use of exf:  o Fixing OPTIONS files for use of exf:
3804    - ALLOW_ECCO not needed    - ALLOW_ECCO not needed
3805    - ECCO_CPPOPTIONS.h should not be included from    - ECCO_CPPOPTIONS.h should not be included from
# Line 2586  o Removed all CPP options for cal packag Line 3813  o Removed all CPP options for cal packag
3813  o modified STOREs in GAD_ADVECTION  o modified STOREs in GAD_ADVECTION
3814  o corrected key comp. for passkey  o corrected key comp. for passkey
3815    
3816  checkpoint52b_post  checkpoint52b_post (2003/11/23)
3817  o new version: "thsice" of thermodynamic sea-ice pkg:  o new version: "thsice" of thermodynamic sea-ice pkg:
3818   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
3819   - modify fluxes but do not change theta directly;   - modify fluxes but do not change theta directly;
# Line 2594  o new version: "thsice" of thermodynamic Line 3821  o new version: "thsice" of thermodynamic
3821   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
3822     + output_thsice.txt to test thsice & bulk_force pkgs.     + output_thsice.txt to test thsice & bulk_force pkgs.
3823  o put back grid & coriolis monitor output.  o put back grid & coriolis monitor output.
3824  checkpoint52b_pre  checkpoint52b_pre (2003/11/23)
3825    
3826  o call "do_the_model_io" at the beginning (=> dump initial state)  o call "do_the_model_io" at the beginning (=> dump initial state)
3827  o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)  o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
# Line 2604  o missing PTRACERS headers in some routi Line 3831  o missing PTRACERS headers in some routi
3831  o default tamc.h in pkg/autodiff supposed to crash  o default tamc.h in pkg/autodiff supposed to crash
3832    to ensure proper customization    to ensure proper customization
3833    
3834  checkpoint52a_post  checkpoint52a_post (2003/11/17)
3835  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
3836    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
3837    - subroutine FREEZE_SURFACE now limits only surface temperature    - subroutine FREEZE_SURFACE now limits only surface temperature
# Line 2619  o fix problem with ECCO-related divided Line 3846  o fix problem with ECCO-related divided
3846    snapshot file was missing some ad-variables,    snapshot file was missing some ad-variables,
3847    but no warning issued by TAF    but no warning issued by TAF
3848    
3849  checkpoint52a_pre  checkpoint52a_pre (2003/11/12)
3850  o some bug fixes for #undef REAL4_IS_SLOW  o some bug fixes for #undef REAL4_IS_SLOW
3851    
3852  checkpoint52 = ecco_c52_e35  checkpoint52 = ecco_c52_e35
3853  o after testing adjoints of checkpoint51u_post  o after testing adjoints of checkpoint51u_post
3854    
3855  checkpoint51u_post  checkpoint51u_post (2003/11/06)
3856  o this is the post-merge tag of the ecco-branch  o this is the post-merge tag of the ecco-branch
3857    (needs another clean checkout and re-testing)    (needs another clean checkout and re-testing)
3858  o various natl_box_adjoint configs and results  o various natl_box_adjoint configs and results
# Line 2640  o top level routines the_main_loop, forw Line 3867  o top level routines the_main_loop, forw
3867    (new namelist ecco_cost_nml)    (new namelist ecco_cost_nml)
3868  o in ctrl/ cleaned some cross-dependencies and updated CPP options  o in ctrl/ cleaned some cross-dependencies and updated CPP options
3869    
3870  checkpoint51t_post  checkpoint51t_post (2003/11/04)
3871  o this is the pre-merge tag of the ecco-branch  o this is the pre-merge tag of the ecco-branch
3872    
3873  checkpoint51s_post  checkpoint51s_post (2003/11/04)
3874  o cleanup: removed various obsolete #define-s  o cleanup: removed various obsolete #define-s
3875  o pkg/grdchk  o pkg/grdchk
3876    - renamed 'ph-grd 3' to 'grad-res'    - renamed 'ph-grd 3' to 'grad-res'
# Line 2652  o pkg/grdchk Line 3879  o pkg/grdchk
3879    - additional high-precision output for testreport    - additional high-precision output for testreport
3880      (grep for 'precision_grdchk_result')      (grep for 'precision_grdchk_result')
3881    
3882  checkpoint51r_post  checkpoint51r_post (2003/11/03)
3883  o cleaned up or removed CPP_OPTIONS.h files  o cleaned up or removed CPP_OPTIONS.h files
3884  o updated results for some of the tests to reflect the new  o updated results for some of the tests to reflect the new
3885    optfiles (-ieee: -O0 instead of -O3)    optfiles (-ieee: -O0 instead of -O3)
3886    
3887  checkpoint51q_post  checkpoint51q_post (2003/10/30)
3888  o cd_code:  o cd_code:
3889    - moved cd_scheme.F -> cd_code_scheme.F    - moved cd_scheme.F -> cd_code_scheme.F
3890    - separate read_checkpoint from cd_code_ini_vars.F    - separate read_checkpoint from cd_code_ini_vars.F
# Line 2673  o ctrl package totally restructured Line 3900  o ctrl package totally restructured
3900    - confined inclusion of AD_CONFIG.h to where necessary.    - confined inclusion of AD_CONFIG.h to where necessary.
3901  o genmake2: changed AD dependencies from SRCFILES to AD_FILES  o genmake2: changed AD dependencies from SRCFILES to AD_FILES
3902    
3903  checkpoint51p_post  checkpoint51p_post (2003/10/30)
3904  o create initial cd_code package  o create initial cd_code package
3905    - WARNING: the initialization of fields within packages    - WARNING: the initialization of fields within packages
3906      is broken because INI_FIELDS (where READ_CHECKPOINT is      is broken because INI_FIELDS (where READ_CHECKPOINT is
# Line 2688  o create initial cd_code package Line 3915  o create initial cd_code package
3915  o cleanup verification/*/code/GMREDI_OPTIONS.h  o cleanup verification/*/code/GMREDI_OPTIONS.h
3916  o cleanup testreport  o cleanup testreport
3917    
3918  checkpoint51o_post  checkpoint51o_post (2003/10/27)
3919  o bringing AD-related verif's up to date with genmake2  o bringing AD-related verif's up to date with genmake2
3920    - carbon/    - carbon/
3921    - global_ocean.90x40x15/    - global_ocean.90x40x15/
# Line 2709  o Correcting initialisations for fVerU, Line 3936  o Correcting initialisations for fVerU,
3936  o helping TAF to recognize dependency on kUp for  o helping TAF to recognize dependency on kUp for
3937    fVerU, fVerV    fVerU, fVerV
3938  o Replacing delZ by delR in pkg/ctrl/  o Replacing delZ by delR in pkg/ctrl/
3939  checkpoint51o_pre  checkpoint51o_pre (2003/10/24)
3940    
3941  o undid all of cp51 pending some cleanups and discussion  o undid all of cp51 pending some cleanups and discussion
3942  o added the [#include "AD_CONFIG.h"] statement to all files that need  o added the [#include "AD_CONFIG.h"] statement to all files that need
# Line 2717  o added the [#include "AD_CONFIG.h"] sta Line 3944  o added the [#include "AD_CONFIG.h"] sta
3944   o re-worked the build logic in genmake2 to support AD_CONFIG.h   o re-worked the build logic in genmake2 to support AD_CONFIG.h
3945   o removed tools/genmake since it no longer works   o removed tools/genmake since it no longer works
3946    
3947  checkpoint51n_post  checkpoint51n_post (2003/10/23)
3948  o modifications to make FREEZE flux visible to pkg/kpp  o modifications to make FREEZE flux visible to pkg/kpp
3949    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
3950    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
# Line 2726  o modifications to make FREEZE flux visi Line 3953  o modifications to make FREEZE flux visi
3953       global_ocean.cs32x15, and global_with_exf)       global_ocean.cs32x15, and global_with_exf)
3954  o added surface flux output variables to TIMEAVE_STATVARS  o added surface flux output variables to TIMEAVE_STATVARS
3955    
3956  checkpoint51n_pre  checkpoint51n_pre (2003/10/23)
3957  o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F  o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
3958  o added [#include "AD_CONFIG.h"] to all files that use the following  o added [#include "AD_CONFIG.h"] to all files that use the following
3959    defines:    defines:
# Line 2734  o added [#include "AD_CONFIG.h"] to all Line 3961  o added [#include "AD_CONFIG.h"] to all
3961    - ALLOW_TANGENTLINEAR_RUN    - ALLOW_TANGENTLINEAR_RUN
3962    - ALLOW_ECCO_OPTIMIZATION    - ALLOW_ECCO_OPTIMIZATION
3963    
3964  checkpoint51m_post  checkpoint51m_post (2003/10/21)
3965  o incorporating changes to get TAMC/TAF working in genmake2  o incorporating changes to get TAMC/TAF working in genmake2
3966    - added new TAMC/TAF targets to the Makefile    - added new TAMC/TAF targets to the Makefile
3967    - various cleanups related to package handling    - various cleanups related to package handling
3968    - these changes should have no impact on the forward model    - these changes should have no impact on the forward model
3969    
3970  checkpoint51l_post  checkpoint51l_post (2003/10/20)
3971  o changes to pkg/cal and pkg/exf that allow and speed-up long integrations  o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
3972   - faster algorithm for cal_addtime.F   - faster algorithm for cal_addtime.F
3973   - higher precision arithmetic, where needed   - higher precision arithmetic, where needed
3974   - pkg/exf *startdate variables changed from calendar date to   - pkg/exf *startdate variables changed from calendar date to
3975     model integration time     model integration time
3976    
3977  checkpoint51l_pre  checkpoint51l_pre (2003/10/17)
3978  o add salt flux to forcing fields (used when salty sea-ice forms or melts)  o add salt flux to forcing fields (used when salty sea-ice forms or melts)
3979  o enable to apply restoring on S & T only in a latitude band.  o enable to apply restoring on S & T only in a latitude band.
3980  o update output (external_forcing_surf modif. change truncation errors)  o update output (external_forcing_surf modif. change truncation errors)
3981     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
3982    
3983  checkpoint51k_post  checkpoint51k_post (2003/10/16)
3984  o change default to: useNHMTerms=.FALSE.  o change default to: useNHMTerms=.FALSE.
3985   - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):   - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
3986     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
# Line 2767  o added an include barrier to the defaul Line 3994  o added an include barrier to the defaul
3994    removed the #include "PACKAGES_CONFIG.h" from it    removed the #include "PACKAGES_CONFIG.h" from it
3995  o fix a bug in mom_fluxform (from chk51j_post)  o fix a bug in mom_fluxform (from chk51j_post)
3996    
3997  checkpoint51j_post  checkpoint51j_post (2003/10/10)
3998  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
3999  o adjusted some flow directives (dynamics, thermodynamics)  o adjusted some flow directives (dynamics, thermodynamics)
4000  o added cubed-sphere case to test cost function  o added cubed-sphere case to test cost function
# Line 2781  o Moving pkg-specific flow directives to Line 4008  o Moving pkg-specific flow directives to
4008         - pkg_ad_diff.list         - pkg_ad_diff.list
4009         - pkg_ad_check_lev?_dir.h         - pkg_ad_check_lev?_dir.h
4010    
4011  checkpoint51i_post  checkpoint51i_post (2003/10/09)
4012  o merge of the branch-genmake2  o merge of the branch-genmake2
4013    - knowingly breaks the older genmake    - knowingly breaks the older genmake
4014    - automatic generation of all ALLOW_${PKG_NAME} defines    - automatic generation of all ALLOW_${PKG_NAME} defines
4015    - new testreport supersedes older testscript    - new testreport supersedes older testscript
4016  o large number of package inclusion and header cleanups  o large number of package inclusion and header cleanups
4017  checkpoint51i_pre  checkpoint51i_pre (2003/10/08)
4018    
4019  o new output for adjoin of global ocean vector invariant  o new output for adjoin of global ocean vector invariant
4020  o fix for checkpoint of thermodynamic seaice and bulk_force  o fix for checkpoint of thermodynamic seaice and bulk_force
# Line 2799  o modify gchem pkg to be more versatile Line 4026  o modify gchem pkg to be more versatile
4026  o modifications to clean up dic pkg  o modifications to clean up dic pkg
4027  o add pkg/cfc  o add pkg/cfc
4028    
4029  checkpoint51g_post  checkpoint51g_post (2003/10/02)
4030  o provide links for ARPACK and ADM*TLM  o provide links for ARPACK and ADM*TLM
4031  o start removing verification/vero/  o start removing verification/vero/
4032  o update AD-related stuff  o update AD-related stuff
# Line 2807  o update AD-related stuff Line 4034  o update AD-related stuff
4034  o adding to verification/global_ocean.90x40x15/ adjoint of  o adding to verification/global_ocean.90x40x15/ adjoint of
4035    vector invariant setup    vector invariant setup
4036    
4037  checkpoint51f_post  checkpoint51f_post (2003/10/02)
4038  o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)  o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
4039  o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation  o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
4040    of tracer Green's fucntions for ocean inversion project.    of tracer Green's fucntions for ocean inversion project.
4041    
4042  checkpoint51f_pre  checkpoint51f_pre (2003/08/07)
4043  o Added on-the-fly spatial interpolation capability  o Added on-the-fly spatial interpolation capability
4044      "USE_EXF_INTERPOLATION" to pkg/exf.      "USE_EXF_INTERPOLATION" to pkg/exf.
4045    - This is a temporary Cartesian-grid hack until    - This is a temporary Cartesian-grid hack until
# Line 2824  o Bug fix to pkg/ptracers, pkg/generic_a Line 4051  o Bug fix to pkg/ptracers, pkg/generic_a
4051      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
4052      non-local transport term.      non-local transport term.
4053    
4054  checkpoint51e_post  checkpoint51e_post (2003/08/03)
4055  o pkg/mom_vecinv:  o pkg/mom_vecinv:
4056    - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)    - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
4057    - add time-ave diagnostic of vorticity advection.    - add time-ave diagnostic of vorticity advection.
# Line 2834  o atmospheric geopotential: - include wa Line 4061  o atmospheric geopotential: - include wa
4061  o land pkg: read initial state from files.  o land pkg: read initial state from files.
4062  o AIM : add stratospheric drag in the upper level  o AIM : add stratospheric drag in the upper level
4063    
4064  checkpoint51d_post  checkpoint51d_post (2003/07/18)
4065  o change function ILNBLNK (=> last non-blank char.) to return zero  o change function ILNBLNK (=> last non-blank char.) to return zero
4066    (instead of the string length) when the string. char is empty    (instead of the string length) when the string. char is empty
4067  o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)  o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
# Line 2847  o Use cluster local disks for purely loc Line 4074  o Use cluster local disks for purely loc
4074    - new active_file_loc... and mdsio_..._loc routines    - new active_file_loc... and mdsio_..._loc routines
4075    - affected packages: autodiff, ctrl, grdchk, mdsio    - affected packages: autodiff, ctrl, grdchk, mdsio
4076    
4077  checkpoint51c_post  checkpoint51c_post (2003/07/08)
4078  o introducing integer flag debugLevel  o introducing integer flag debugLevel
4079    - debLevZero: suppress all output    - debLevZero: suppress all output
4080    - debLevA: standard    - debLevA: standard
# Line 2870  o added verification for adjoint with pt Line 4097  o added verification for adjoint with pt
4097    - checked tapelev/comlev recomputations: OK    - checked tapelev/comlev recomputations: OK
4098  <<<checkpoint51b_pre  <<<checkpoint51b_pre
4099    
4100  checkpoint51a_post  checkpoint51a_post (2003/06/25)
4101  o added code for biogeochemistry package  o added code for biogeochemistry package
4102    - new pkgs: dic, gchem    - new pkgs: dic, gchem
4103    - new subroutine in ptracers    - new subroutine in ptracers
4104  o modify code for biogeo packages  o modify code for biogeo packages
4105    - in model/src and pkg/ptracers    - in model/src and pkg/ptracers
4106    
4107  checkpoint51  checkpoint51 (2003/06/24)
4108  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
4109    - autodiff, ctrl, exf, grdchk, seaice    - autodiff, ctrl, exf, grdchk, seaice
4110    kept separate packages    kept separate packages
# Line 2885  o merged improved packages from ecco-bra Line 4112  o merged improved packages from ecco-bra
4112  o updating verification/internal_wave, verification/lab_sea  o updating verification/internal_wave, verification/lab_sea
4113    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
4114    
4115  checkpoint50i_post  checkpoint50i_post (2003/06/23)
4116  o Preparing next differentiable checkpoint and sync  o Preparing next differentiable checkpoint and sync
4117    of MAIN vs. ecco-branch    of MAIN vs. ecco-branch
4118    - 1st step: this one is differentiable    - 1st step: this one is differentiable
4119    - 2nd step: next(! not this) checkpoint will have updated packages    - 2nd step: next(! not this) checkpoint will have updated packages
4120                from ecco-branch)                from ecco-branch)
4121    
4122  checkpoint50h_post  checkpoint50h_post (2003/06/20)
4123  o new package "land": provide surface BC for AIM.  o new package "land": provide surface BC for AIM.
4124  o pkg/ptracers: apply exchange to all tracers after reading a pickup.  o pkg/ptracers: apply exchange to all tracers after reading a pickup.
4125  o AIM: use true log-P extrapolation for near surface temp (= as in  o AIM: use true log-P extrapolation for near surface temp (= as in
# Line 2901  o New variable in PARM03 for more flexib Line 4128  o New variable in PARM03 for more flexib
4128  o somewhat cleaned package initialisation sequence for  o somewhat cleaned package initialisation sequence for
4129    ctrl/ cost/ ecco/ in packages_... routines    ctrl/ cost/ ecco/ in packages_... routines
4130    
4131  checkpoint50g_post  checkpoint50g_post (2003/05/23)
4132  o merged with release1_p17 (pkg/seaice and verification/lab_sea)  o merged with release1_p17 (pkg/seaice and verification/lab_sea)
4133    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
4134    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
4135      made the default because of faster convergence than ADI      made the default because of faster convergence than ADI
4136    
4137  checkpoint50f_post  checkpoint50f_post (2003/05/23)
4138  o exf totally restructured  o exf totally restructured
4139    - replaced all exf_set_ routines by one generic exf_set_gen.F    - replaced all exf_set_ routines by one generic exf_set_gen.F
4140      and made sure it's still differentiable      and made sure it's still differentiable
# Line 2915  o exf totally restructured Line 4142  o exf totally restructured
4142    - exf_inscal_/exf_outscal_ suffixes consistent with field names    - exf_inscal_/exf_outscal_ suffixes consistent with field names
4143    - updated adjoint/makefile and relevant verif. accordingly    - updated adjoint/makefile and relevant verif. accordingly
4144    
4145  checkpoint50f_pre  checkpoint50f_pre (2003/05/23)
4146   o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;   o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
4147        + change Evap over land. (update aim.5l_cs output)        + change Evap over land. (update aim.5l_cs output)
4148   o added missing .cvsignores and made uniform across expts   o added missing .cvsignores and made uniform across expts
# Line 2925  checkpoint50f_pre Line 4152  checkpoint50f_pre
4152   o new fn in pkg/monitor to stop model if solution grows too big   o new fn in pkg/monitor to stop model if solution grows too big
4153   o removed lots of single quotes from comments   o removed lots of single quotes from comments
4154    
4155  checkpoint50e_post  checkpoint50e_post (2003/05/14)
4156  o make KPP work with PTRACERS  o make KPP work with PTRACERS
4157   - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is   - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
4158     nearly a copy of kpp_transport_s     nearly a copy of kpp_transport_s
4159   - there is no analogue to SurfaceTendencyS, so I have to use   - there is no analogue to SurfaceTendencyS, so I have to use
4160     gPtr(of the surface layer) instead     gPtr(of the surface layer) instead
4161  o add a new platform SunFire+mpi (SunFire 15000) to genmake  o add a new platform SunFire+mpi (SunFire 15000) to genmake
4162  checkpoint50e_pre  checkpoint50e_pre (2003/05/13)
4163    
4164  checkpoint50d_post  checkpoint50d_post (2003/05/13)
4165  o change kpp output from multiple-record state files to single-record state  o change kpp output from multiple-record state files to single-record state
4166    files analogous to write_state.F    files analogous to write_state.F
4167  o reduce the output frequency of cg3d-related stuff to the monitor frequency,  o reduce the output frequency of cg3d-related stuff to the monitor frequency,
4168    analogous to the cg2d-related output.    analogous to the cg2d-related output.
4169  o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,  o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
4170    so that writing to internal file fn (with length 512) fails.    so that writing to internal file fn (with length 512) fails.
4171  checkpoint50d_pre  checkpoint50d_pre (2003/05/12)
4172    
4173  checkpoint50c_post  checkpoint50c_post (2003/05/12)
4174  o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)  o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
4175  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
4176  o add time-average diagnostic of U*V and vertical diffusive flux for theta.  o add time-average diagnostic of U*V and vertical diffusive flux for theta.
4177  o bug fixed in convective adjustment diagnostic (multi-tile set-up).  o bug fixed in convective adjustment diagnostic (multi-tile set-up).
4178  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
4179    
4180  checkpoint50c_pre  checkpoint50c_pre (2003/04/30)
4181  Merging from release1_p13:  Merging from release1_p13:
4182  o bug fix for pkg/seaice dynamic solver  o bug fix for pkg/seaice dynamic solver
4183  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
4184    
4185  checkpoint50b_post  checkpoint50b_post (2003/04/17)
4186  o store u*,v* in gU,V instead of in guNm1,gvNm1  o store u*,v* in gU,V instead of in guNm1,gvNm1
4187  o in order to put the momForcing out of the Adams-Bashforth:  o in order to put the momForcing out of the Adams-Bashforth:
4188    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
# Line 2964  o new flag "useCDscheme" (default=F); re Line 4191  o new flag "useCDscheme" (default=F); re
4191  o re-generate output for highly sensitive test-exp:  o re-generate output for highly sensitive test-exp:
4192     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
4193    
4194  checkpoint50b_pre  checkpoint50b_pre (2003/04/17)
4195  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
4196  o corrected CPP option mismatch in exf_Bulk... functions for case  o corrected CPP option mismatch in exf_Bulk... functions for case
4197    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
4198    
4199  checkpoint50a_post  checkpoint50a_post (2003/03/21)
4200  o Bug fix for merging between c50 and KPP.  o Bug fix for merging between c50 and KPP.
4201    ikey was passed from thermodynamics to kpp_calc via    ikey was passed from thermodynamics to kpp_calc via
4202    common block rather than being recomputed in kpp_calc,    common block rather than being recomputed in kpp_calc,
4203    in contradiction with new key itdkey.    in contradiction with new key itdkey.
4204    New key ikppkey created, and tamc.h headers updated.    New key ikppkey created, and tamc.h headers updated.
4205    
4206  checkpoint50  checkpoint50 (2003/03/08)
4207  - 2nd step of merge with ecco-branch:  - 2nd step of merge with ecco-branch:
4208    merge changes in ecco-branch back into main trunk    merge changes in ecco-branch back into main trunk
4209  - bug fix in find_alpha  - bug fix in find_alpha
# Line 2984  checkpoint50 Line 4211  checkpoint50
4211  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
4212  - merged some sliced AD support routines  - merged some sliced AD support routines
4213    
4214  checkpoint49  checkpoint49 (2003/03/06)
4215  merged from ecco-branch:  merged from ecco-branch:
4216  o exf:  o exf:
4217    - Enable initialisation of forcing fields to constant    - Enable initialisation of forcing fields to constant
# Line 3022  o DIVA: Line 4249  o DIVA:
4249    (see MITgcm manual).    (see MITgcm manual).
4250  o cal: synchronized between MAIN and ecco-branch  o cal: synchronized between MAIN and ecco-branch
4251    
4252  checkpoint48i_post  checkpoint48i_post (2003/03/05)
4253  o Changes to restore differentiability of code w.r.t. previous tag  o Changes to restore differentiability of code w.r.t. previous tag
4254    (mostly adding new routines to make list and replacing    (mostly adding new routines to make list and replacing
4255    pressure by totPhiHyd).    pressure by totPhiHyd).
# Line 3040  o Modif. for DIVA: Line 4267  o Modif. for DIVA:
4267    tbar, sbar, psbar, which should not be reinitialised;    tbar, sbar, psbar, which should not be reinitialised;
4268    only relevant for ecco-branch)    only relevant for ecco-branch)
4269    
4270  checkpoint48h_post  checkpoint48h_post (2003/02/28)
4271  o improve "ini_p_ground" when using finite difference form for calc_phi_hyd  o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
4272  o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F  o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
4273  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
4274  o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT  o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
4275    
4276  checkpoint48g_post  checkpoint48g_post (2003/02/18)
4277  --- EOS:  --- EOS:
4278  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
4279    store total Potential in totPhyHyd for diagnostics & EOS.    store total Potential in totPhyHyd for diagnostics & EOS.
# Line 3060  o accurate phiHyd when using interface-W Line 4287  o accurate phiHyd when using interface-W
4287   ( changes results of ideal_2D_oce )   ( changes results of ideal_2D_oce )
4288  o includes r* 2nd term in potential gradient.  o includes r* 2nd term in potential gradient.
4289    
4290  checkpoint48f_post  checkpoint48f_post (2003/02/18)
4291  Merging from release1_p12:  Merging from release1_p12:
4292  o Modifications for using pkg/exf with pkg/seaice  o Modifications for using pkg/exf with pkg/seaice
4293    - improved description of the various forcing configurations    - improved description of the various forcing configurations
# Line 3088  o pkg/seaice: Line 4315  o pkg/seaice:
4315    - adjoint-friendly modifications    - adjoint-friendly modifications
4316    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
4317    
4318  checkpoint48e_post  checkpoint48e_post (2003/02/12)
4319  o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)  o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
4320  o dynamics: change definition of computational domain & adapt mom_fluxform  o dynamics: change definition of computational domain & adapt mom_fluxform
4321    accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.    accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
# Line 3099  o following exp works with Olx=Oly=2 (an Line 4326  o following exp works with Olx=Oly=2 (an
4326      inverted_barometer solid-body.cs-32x32x1      inverted_barometer solid-body.cs-32x32x1
4327    (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)    (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
4328    
4329  checkpoint48d_post  checkpoint48d_post (2003/02/09)
4330  o in preparation for r*:  o in preparation for r*:
4331   a) use pre-computed gradient of hydrostatic potential:   a) use pre-computed gradient of hydrostatic potential:
4332      changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce      changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
# Line 3107  o in preparation for r*: Line 4334  o in preparation for r*:
4334      => affects results of glob_oce_pressure (different truncation error)        => affects results of glob_oce_pressure (different truncation error)  
4335    update output.txt of ideal_2D_oce & global_ocean_pressure    update output.txt of ideal_2D_oce & global_ocean_pressure
4336    
4337  checkpoint48d_pre  checkpoint48d_pre (2003/02/08)
4338  o in preparation for r*:  o in preparation for r*:
4339    new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.    new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
4340    pass the 2 comp. of the grad. as arguments to momentum S/R.    pass the 2 comp. of the grad. as arguments to momentum S/R.
4341    but for the moment, only used if it does not change the results.    but for the moment, only used if it does not change the results.
4342  o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP  o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
4343    
4344  checkpoint48c_post  checkpoint48c_post (2003/02/06)
4345  Modifications in treatment of initial flux forcing controls  Modifications in treatment of initial flux forcing controls
4346  to avoid extra storing of flux fields.  to avoid extra storing of flux fields.
4347    
4348  checkpoint48c_pre  checkpoint48c_pre (2003/01/21)
4349  o Added tidal_basin_2d experiment (currently 1D!)  o Added tidal_basin_2d experiment (currently 1D!)
4350  o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)  o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
4351    
4352  checkpoint48b_post  checkpoint48b_post (2003/01/27)
4353  o r* coordinate added in #ifdef NONLIN_FRSURF block.  o r* coordinate added in #ifdef NONLIN_FRSURF block.
4354   (modification to pressure gradient not yet implemented)   (modification to pressure gradient not yet implemented)
4355  o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports  o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
4356    (for U & V) that are used for vertical advection of momentum.    (for U & V) that are used for vertical advection of momentum.
4357    
4358  checkpoint48a_post  checkpoint48a_post (2003/01/24)
4359  o In preparation for r*, use temp. array to compute vertical transport  o In preparation for r*, use temp. array to compute vertical transport
4360     in flux-form momentum pkg. => change results of few test-exp.     in flux-form momentum pkg. => change results of few test-exp.
4361    Update output of: exp4, exp5, front_relax, global_ocean_pressure,    Update output of: exp4, exp5, front_relax, global_ocean_pressure,
4362                      lab_sea, natl_box & plume_on_slope                      lab_sea, natl_box & plume_on_slope
4363    
4364  checkpoint48  checkpoint48 (2003/01/23)
4365  o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')  o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
4366    
4367  checkpoint47j_post  checkpoint47j_post (2003/01/21)
4368  o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.  o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
4369  o moved adexch from forward_step to addummy_in_stepping  o moved adexch from forward_step to addummy_in_stepping
4370  o added exch in ctrl_map_...  o added exch in ctrl_map_...
# Line 3156  o Yet more changes in gmredi: Line 4383  o Yet more changes in gmredi:
4383      re-activated full calculation of taperfct for case 'ac02'      re-activated full calculation of taperfct for case 'ac02'
4384  o updating verification/ adjoints of carbon, global_ocean.90x40x15  o updating verification/ adjoints of carbon, global_ocean.90x40x15
4385    
4386  checkpoint47i_post  checkpoint47i_post (2003/01/13)
4387  o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.  o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
4388  o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)  o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
4389    default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)    default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
# Line 3172  o case GM_BOLUS_ADVEC should be cleaned Line 4399  o case GM_BOLUS_ADVEC should be cleaned
4399    S/R gmredi_slope_psi should be cleaned    S/R gmredi_slope_psi should be cleaned
4400  o verification/carbon now has exactConserv=.TRUE.  o verification/carbon now has exactConserv=.TRUE.
4401    
4402  checkpoint47g_post  checkpoint47g_post (2003/01/10)
4403  o time-average AIM output: becomes independent from statvars time-average  o time-average AIM output: becomes independent from statvars time-average
4404    (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)    (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
4405  o After TAF bug fix:  o After TAF bug fix:
# Line 3198  Gradient checks OK for Line 4425  Gradient checks OK for
4425  in conjunction with data.gmredi parameters to be checked in  in conjunction with data.gmredi parameters to be checked in
4426  in a few minutes under verification/carbon/code/  in a few minutes under verification/carbon/code/
4427    
4428  checkpoint47f_post  checkpoint47f_post (2002/12/28)
4429  Merging from release1_p10:  Merging from release1_p10:
4430  o modifications for using pkg/exf with pkg/seaice  o modifications for using pkg/exf with pkg/seaice
4431    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
# Line 3210  o modifications for using pkg/exf with p Line 4437  o modifications for using pkg/exf with p
4437    - verification/lab_sea default experiment now uses    - verification/lab_sea default experiment now uses
4438      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
4439    
4440  checkpoint47e_post  checkpoint47e_post (2002/12/27)
4441  o created a tag prior to creating a branch  o created a tag prior to creating a branch
4442    
4443  checkpoint47d_post  checkpoint47d_post (2002/12/16)
4444  o fixed bug in the oceanic pressure coordinates code: vertical viscosity  o fixed bug in the oceanic pressure coordinates code: vertical viscosity
4445    at the bottom boundary had an erroneous half slip boundary condition    at the bottom boundary had an erroneous half slip boundary condition
4446  o added bottom drag and no slip boundary condition capabilities to  o added bottom drag and no slip boundary condition capabilities to
4447    oceanic pressure coordinates code    oceanic pressure coordinates code
4448  o added new verification experiment global_ocean_pressure, this experiment is  o added new verification experiment global_ocean_pressure, this experiment is
4449    also described in the tutorial section of the manual    also described in the tutorial section of the manual
4450  checkpoint47d_pre  checkpoint47d_pre (2002/12/16)
4451    
4452  checkpoint47c_post  checkpoint47c_post (2002/12/16)
4453  o Added a verification experiment for a global cubed-sphere ocean run  o Added a verification experiment for a global cubed-sphere ocean run
4454    -  verification/global_ocean.cubed32x32x30    -  verification/global_ocean.cubed32x32x30
4455    -  uses pkg/therm_seaice and pkg/bulk_forcing    -  uses pkg/therm_seaice and pkg/bulk_forcing
# Line 3234  o OCEANICP & realFreshWater: include P-E Line 4461  o OCEANICP & realFreshWater: include P-E
4461    NOTES: requires option NONLIN_FRSURF to be "#define".    NOTES: requires option NONLIN_FRSURF to be "#define".
4462  o update advect_xz/results/output.txt (left from checkpoint44g_post)  o update advect_xz/results/output.txt (left from checkpoint44g_post)
4463    
4464  checkpoint47b_post  checkpoint47b_post (2002/12/05)
4465  Merging from release1_p9:  Merging from release1_p9:
4466  o pkg/seaice  o pkg/seaice
4467    - removed GOTO's and added taf directives    - removed GOTO's and added taf directives
# Line 3251  o verification/lab_sea Line 4478  o verification/lab_sea
4478    - added missing matlab routines    - added missing matlab routines
4479    - added test of thermodynamics parallelization    - added test of thermodynamics parallelization
4480    
4481  checkpoint47a_post  checkpoint47a_post (2002/11/23)
4482  o new pkg: aim_v23  o new pkg: aim_v23
4483   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
4484     for now, keep the same surface forcing as before.     for now, keep the same surface forcing as before.
# Line 3268  o bulk_force and therm_seaice Line 4495  o bulk_force and therm_seaice
4495  - Two ifdef statements for compile time,  - Two ifdef statements for compile time,
4496     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
4497    
4498  checkpoint47  checkpoint47 (2002/11/15)
4499  differentiable version of checkpoint46n_post  differentiable version of checkpoint46n_post
4500  o bug fix in quasihydrostaticterms  o bug fix in quasihydrostaticterms
4501  o * "clean" adjoint code (in terms of extensive recomputations)  o * "clean" adjoint code (in terms of extensive recomputations)
# Line 3297  o Updated verification/carbon/ Line 4524  o Updated verification/carbon/
4524    - #define GM_VISBECK_VARIABLE_K    - #define GM_VISBECK_VARIABLE_K
4525    - GM_taper_scheme    = 'ldd97'        - GM_taper_scheme    = 'ldd97'    
4526    
4527  checkpoint46n_post  checkpoint46n_post (2002/11/12)
4528  Merging from release1_p8:  Merging from release1_p8:
4529  o verification/natl_box:  o verification/natl_box:
4530    updating new external_fields_load routine    updating new external_fields_load routine
# Line 3351  o Adding new verification experiment glo Line 4578  o Adding new verification experiment glo
4578    the exf (and cal) package instead of the    the exf (and cal) package instead of the
4579    external_fields_load routine (cf README file).    external_fields_load routine (cf README file).
4580    
4581  checkpoint46m_post  checkpoint46m_post (2002/11/07)
4582  o modified testscript to return -- when there are no lines of "%MON" output  o modified testscript to return -- when there are no lines of "%MON" output
4583  o added new flag "quasiHydrostatic" for QH mode  o added new flag "quasiHydrostatic" for QH mode
4584    and new routine quasihydrostaticterms()    and new routine quasihydrostaticterms()
# Line 3364  o introduced flag for controllin non-hyd Line 4591  o introduced flag for controllin non-hyd
4591  o removed gravitySign from PARM04  o removed gravitySign from PARM04
4592  o switched to g77/ifc from pgf77 in aim experiments  o switched to g77/ifc from pgf77 in aim experiments
4593    
4594  checkpoint46l_post  checkpoint46l_post (2002/11/01)
4595  o made convective adjustment work with pressure coordinates:  o made convective adjustment work with pressure coordinates:
4596   - changed the direction of k-loop in convective_adjustment.F for the   - changed the direction of k-loop in convective_adjustment.F for the
4597     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
# Line 3377  o made convective adjustment work with p Line 4604  o made convective adjustment work with p
4604     at the beginning of find_rho, find_alpha, and find_beta, does a     at the beginning of find_rho, find_alpha, and find_beta, does a
4605     check of the entire slice, if CPP-option     check of the entire slice, if CPP-option
4606     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
4607  checkpoint46l_pre  checkpoint46l_pre (2002/10/23)
4608    
4609  checkpoint46k_post  checkpoint46k_post (2002/10/23)
4610  o fixed the verification/global_ocean.90x40x15 experiment:  o fixed the verification/global_ocean.90x40x15 experiment:
4611   - new bathymetry (the world according to A., JMC, and M.)   - new bathymetry (the world according to A., JMC, and M.)
4612   - new initial fields and forcing fields (*.bin files)   - new initial fields and forcing fields (*.bin files)
# Line 3393  o S/R aim_initialise.F replace S/R aim_i Line 4620  o S/R aim_initialise.F replace S/R aim_i
4620   - read AIM physics parameters from a file (data.aimphys)   - read AIM physics parameters from a file (data.aimphys)
4621   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
4622    
4623  checkpoint46j_post  checkpoint46j_post (2002/10/07)
4624  o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH  o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
4625  o move wVel computation at the end of the time step, in S/R integr_continuity  o move wVel computation at the end of the time step, in S/R integr_continuity
4626  o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)  o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
4627  o update timeave pkg for wVel diagnostic.  o update timeave pkg for wVel diagnostic.
4628  checkpoint46j_pre  checkpoint46j_pre (2002/09/27)
4629    
4630  checkpoint46i_post  checkpoint46i_post (2002/09/25)
4631  o Clean up AIM package (and keep the results unchanged):  o Clean up AIM package (and keep the results unchanged):
4632    include CPP_OPTION and use IMPLICT NONE in all routines ;    include CPP_OPTION and use IMPLICT NONE in all routines ;
4633    declare all the variables _RL ; use _d 0 for all numerical constants.    declare all the variables _RL ; use _d 0 for all numerical constants.
4634    use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !    use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
4635    
4636  checkpoint46h_post  checkpoint46h_post (2002/09/25)
4637  o cleaned up the use of rhoNil and rhoConst.  o cleaned up the use of rhoNil and rhoConst.
4638    - rhoNil should only appear in the LINEAR equation of state, everywhere    - rhoNil should only appear in the LINEAR equation of state, everywhere
4639      else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst      else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
# Line 3416  o introduced new parameter rhoConstFresh Line 4643  o introduced new parameter rhoConstFresh
4643    value is 999.8 kg/m^3    value is 999.8 kg/m^3
4644  o cleanup up external_forcing.F and external_forcing_surf.F  o cleanup up external_forcing.F and external_forcing_surf.F
4645    - can now be used by both OCEANIC and OCEANICP    - can now be used by both OCEANIC and OCEANICP
4646  checkpoint46h_pre  checkpoint46h_pre (2002/09/18)
4647    
4648   Added code to convert surface volume flux (fresh water) into   Added code to convert surface volume flux (fresh water) into
4649   a mass flux when using P coordinates in the ocean (OCEANICP).   a mass flux when using P coordinates in the ocean (OCEANICP).
4650   Note: It assumes you have set rho0=rhoConst=density of fresh water.   Note: It assumes you have set rho0=rhoConst=density of fresh water.
4651    
4652  checkpoint46g_post  checkpoint46g_post (2002/09/18)
4653  o Include a new diagnostic variable phiHydLow for the ocean model  o Include a new diagnostic variable phiHydLow for the ocean model
4654    - in z-coordinates, it is the bottom pressure anomaly    - in z-coordinates, it is the bottom pressure anomaly
4655    - in p-coordinates, it is the sea surface elevation    - in p-coordinates, it is the sea surface elevation
# Line 3440  o cleaned up find_rho Line 4667  o cleaned up find_rho
4667    - removed obsolete 'eqn' from the parameter list.    - removed obsolete 'eqn' from the parameter list.
4668  o added two new verification experiments: gop and goz  o added two new verification experiments: gop and goz
4669    (4x4 degree global ocean, 15 layers in pressure and height coordinates)    (4x4 degree global ocean, 15 layers in pressure and height coordinates)
4670  checkpoint46g_pre  checkpoint46g_pre (2002/09/16)
4671    
4672  checkpoint46f_post  checkpoint46f_post (2002/09/16)
4673  o Enable tangent linear (forward mode) gradient checks:  o Enable tangent linear (forward mode) gradient checks:
4674    - extended active file handling to g_... files    - extended active file handling to g_... files
4675    - added TANGENT_SIMULATION to theSimulationMode    - added TANGENT_SIMULATION to theSimulationMode
# Line 3450  o Enable tangent linear (forward mode) g Line 4677  o Enable tangent linear (forward mode) g
4677  o added tangent linear setup in verification/carbon/code_ftl  o added tangent linear setup in verification/carbon/code_ftl
4678  o added adjoint setup in verification/front_relax/code_ad  o added adjoint setup in verification/front_relax/code_ad
4679    
4680  checkpoint46e_post  checkpoint46e_post (2002/09/05)
4681  o Added new equation of state -> MDJWF  o Added new equation of state -> MDJWF
4682    - EOS of McDougall et al., 2002, JAOT, submitted    - EOS of McDougall et al., 2002, JAOT, submitted
4683    - caveat: the equation of state is only valid for a smaller (more    - caveat: the equation of state is only valid for a smaller (more
# Line 3459  o Added new equation of state -> MDJWF Line 4686  o Added new equation of state -> MDJWF
4686    - added more check values for density in check_eos (ini_eos.F), some of    - added more check values for density in check_eos (ini_eos.F), some of
4687      the old check values are out of the range of the MDJWF-eos, so don't      the old check values are out of the range of the MDJWF-eos, so don't
4688      expect perfect matches for those      expect perfect matches for those
4689  checkpoint46e_pre  checkpoint46e_pre (2002/08/19)
4690    
4691  checkpoint46d_post  checkpoint46d_post (2002/08/19)
4692  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
4693    'OCEANICP', also initialised field pressure correctly in ini_eos in the    'OCEANICP', also initialised field pressure correctly in ini_eos in the
4694    case of pressure coordinates. eosType='JMD95Z' in    case of pressure coordinates. eosType='JMD95Z' in
4695    combination with buoyancyRelation='OCEANICP' now causes an error.    combination with buoyancyRelation='OCEANICP' now causes an error.
4696  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
4697    in find_alpha/beta.    in find_alpha/beta.
4698  checkpoint46d_pre  checkpoint46d_pre (2002/08/15)
4699    
4700  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
4701    so that JMD95Z and JMD95P give approptiate static stability in find_rho.    so that JMD95Z and JMD95P give approptiate static stability in find_rho.
4702    
4703  checkpoint46c_post  checkpoint46c_post (2002/08/15)
4704  o Changes necessary for ocean in p-coordinates  o Changes necessary for ocean in p-coordinates
4705   -  Added new buoyancy relation = 'OCEANICP'   -  Added new buoyancy relation = 'OCEANICP'
4706   -  Added new parameters = gravitySign (this used to be contained inside   -  Added new parameters = gravitySign (this used to be contained inside
4707      the factor dRdZ which I added when we first switched to R coordinates).      the factor dRdZ which I added when we first switched to R coordinates).
4708   X GM/Redi is not compatible (yet)   X GM/Redi is not compatible (yet)
4709   X bottom drag and no-slip need to be debugged.   X bottom drag and no-slip need to be debugged.
4710  checkpoint46c_pre  checkpoint46c_pre (2002/08/07)
4711    
4712  checkpoint46b_post  checkpoint46b_post (2002/08/07)
4713  o Added new equation of state -> JMD95Z and JMD95P  o Added new equation of state -> JMD95Z and JMD95P
4714    - EOS of Jackett and McDougall, 1995, JAOT    - EOS of Jackett and McDougall, 1995, JAOT
4715    - moved all EOS parameters into EOS.h    - moved all EOS parameters into EOS.h
# Line 3491  o Added UNESCO EOS, but not recommended Line 4718  o Added UNESCO EOS, but not recommended
4718    in-situ temperature (see JMD95)    in-situ temperature (see JMD95)
4719  o Modified formatting for knudsen2.f in utils/knudsen2 and added  o Modified formatting for knudsen2.f in utils/knudsen2 and added
4720    unesco.f to be used with POLY3    unesco.f to be used with POLY3
4721  checkpoint46b_pre  checkpoint46b_pre (2002/07/31)
4722    
4723  checkpoint46a_post  checkpoint46a_post (2002/07/31)
4724  o Added (atmospheric) pressure loading  o Added (atmospheric) pressure loading
4725    - new field in FFIELDS.h, etc...    - new field in FFIELDS.h, etc...
4726    - new cpp flag ATMOSPHERIC_LOADING    - new cpp flag ATMOSPHERIC_LOADING
4727  o Changed hFacC to _hFacC in calc_phi_hyd.F  o Changed hFacC to _hFacC in calc_phi_hyd.F
4728  o Added SHORTWAVE_HEATING to some files for consistency  o Added SHORTWAVE_HEATING to some files for consistency
4729  checkpoint46a_pre  checkpoint46a_pre (2002/07/13)
4730    
4731  checkpoint46  checkpoint46 (2002/07/13)
4732  further merges from release1_p5  further merges from release1_p5
4733  o new ctrl package  o new ctrl package
4734    - adopted from ECCO environment to enable optimization    - adopted from ECCO environment to enable optimization
# Line 3528  o added hooks for Eliassen Palm fluxes ( Line 4755  o added hooks for Eliassen Palm fluxes (
4755  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
4756  o incorporated hooks for sponge layer code (external_forcing.F)  o incorporated hooks for sponge layer code (external_forcing.F)
4757    
4758  checkpoint45d_post  checkpoint45d_post (2002/07/12)
4759  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
4760  o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S  o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
4761    (affects plume_on_slope "cg2d" output)    (affects plume_on_slope "cg2d" output)
# Line 3542  o add new flags: Line 4769  o add new flags:
4769   - for each tracer, define internal flag for multiDimAdvection & A-B   - for each tracer, define internal flag for multiDimAdvection & A-B
4770  o monitor: change definition of KE to check conservation of Energy  o monitor: change definition of KE to check conservation of Energy
4771    
4772  checkpoint45c_post  checkpoint45c_post (2002/05/30)
4773  o Removed f90 comments ("!")  o Removed f90 comments ("!")
4774  o Modified initialisations to enable exf package for MITgcm  o Modified initialisations to enable exf package for MITgcm
4775    (without invoking ECCO_PACKAGE).    (without invoking ECCO_PACKAGE).
# Line 3550  o modifications to gradient check packag Line 4777  o modifications to gradient check packag
4777    - enable centered differences    - enable centered differences
4778    - modified format of standard output    - modified format of standard output
4779    
4780  checkpoint45b_post  checkpoint45b_post (2002/05/30)
4781  o cleaned exchange calls in cg2d  o cleaned exchange calls in cg2d
4782  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
4783  o included CPP option SINGLE_LAYER_MODE in thermodynamics  o included CPP option SINGLE_LAYER_MODE in thermodynamics
# Line 3562  o in initialise_varia, moved call packag Line 4789  o in initialise_varia, moved call packag
4789    (corresponding adjustment of TAF tape initialisation).    (corresponding adjustment of TAF tape initialisation).
4790  o in calc_diffusivity/calc_viscosity extended domain to full overlap.  o in calc_diffusivity/calc_viscosity extended domain to full overlap.
4791    
4792  checkpoint45a_post  checkpoint45a_post (2002/05/01)
4793  o compute Rho over the whole domain (extend iMin,jMin indices)  o compute Rho over the whole domain (extend iMin,jMin indices)
4794  o specific exchange for X-slice domain (case Ny=1)  o specific exchange for X-slice domain (case Ny=1)
4795  o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code  o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
# Line 3582  o errorMessageUnit set non-equal zero in Line 4809  o errorMessageUnit set non-equal zero in
4809    (conflict on some platforms, e.g. IBM SP3)    (conflict on some platforms, e.g. IBM SP3)
4810  o modified carbon verif.  o modified carbon verif.
4811    
4812  checkpoint44h_pre  checkpoint44h_pre (2002/03/14)
4813  o vertical grid option: allow to put the Interface at the middle between  o vertical grid option: allow to put the Interface at the middle between
4814    2 cell-centers ; replace delZ in pkg/kpp by drF.    2 cell-centers ; replace delZ in pkg/kpp by drF.
4815  o GM Advective form: Tracers are advected using the residual transport (=  o GM Advective form: Tracers are advected using the residual transport (=
4816    Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.    Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
4817    
4818  checkpoint44g_post  checkpoint44g_post (2002/03/05)
4819  o fix surface correction term in multiDimAdvection (affects plume_on_slope  o fix surface correction term in multiDimAdvection (affects plume_on_slope
4820    results) ; ifdef missing in thermodynamics.F    results) ; ifdef missing in thermodynamics.F
4821    
# Line 3653  o merge of relevant stuff from the ecco- Line 4880  o merge of relevant stuff from the ecco-
4880  o check parameters & config (chkpt44a_pre,post)  o check parameters & config (chkpt44a_pre,post)
4881  o OBC and NonLin_FrSurf.  o OBC and NonLin_FrSurf.
4882    
4883  checkpoint44  checkpoint44 (2002/01/18)
4884  o fix bug in mom_vi_del2uv  o fix bug in mom_vi_del2uv
4885  o select when filters are applied ; add options to zonal_filter (data.zonfilt)  o select when filters are applied ; add options to zonal_filter (data.zonfilt)
4886  o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)  o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
# Line 3661  o update AIM experiments (NCEP input fil Line 4888  o update AIM experiments (NCEP input fil
4888  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
4889  o added some stuff for AD  o added some stuff for AD
4890    
4891  checkpoint43  checkpoint43 (2001/09/28)
4892  o added two new advection tests  o added two new advection tests
4893  o added global 4x4 degree ocean test  o added global 4x4 degree ocean test
4894  o added test of H&S94 with free surface on cube  o added test of H&S94 with free surface on cube
4895  o some final mods for gradient check, adjoint,...  o some final mods for gradient check, adjoint,...
4896    
4897  checkpoint42  checkpoint42 (2001/09/27)
4898    Fixed AD-related problems:    Fixed AD-related problems:
4899  o Store directives up-to-date with re-arranged Adams-Bashforth  o Store directives up-to-date with re-arranged Adams-Bashforth
4900    (mainly thermodynamics.F)    (mainly thermodynamics.F)
# Line 3679  o Modified store directives for split of Line 4906  o Modified store directives for split of
4906    for the case ALLOW_KPP    for the case ALLOW_KPP
4907  o Cleaned argument list for timestep_tracer.F  o Cleaned argument list for timestep_tracer.F
4908    
4909  checkpoint41  checkpoint41 (2001/09/27)
4910  o re-formatted/added comments in prologues of key subroutines  o re-formatted/added comments in prologues of key subroutines
4911    to work with protex    to work with protex
4912    
4913  checkpoint40  checkpoint40 (2001/09/27)
4914  o moved calc_gs, calc_gt and calc_tr1 back to model/src  o moved calc_gs, calc_gt and calc_tr1 back to model/src
4915  o added FLT (floats) package from Arne along with demo. experiment  o added FLT (floats) package from Arne along with demo. experiment
4916  o re-arranged Adams-Bashforth scheme for tracers to allow easier  o re-arranged Adams-Bashforth scheme for tracers to allow easier
# Line 3692  o more mods for non-linear free-surface Line 4919  o more mods for non-linear free-surface
4919  o modified multi-dim method to work on cube  o modified multi-dim method to work on cube
4920  o bug fix in KPP (from DM)  o bug fix in KPP (from DM)
4921    
4922  checkpoint40pre9  checkpoint40pre9 (2001/09/27)
4923  o added DST advection schemes  o added DST advection schemes
4924  o fix MPI bug on SGI's  o fix MPI bug on SGI's
4925  o modifications for non-linear free-surface  o modifications for non-linear free-surface
# Line 3702  o changes to commenting of arguments for Line 4929  o changes to commenting of arguments for
4929  o added/updated many matlab scripts  o added/updated many matlab scripts
4930  o added multi-dimensional advection method for tracers  o added multi-dimensional advection method for tracers
4931        
4932  checkpoint40pre8  checkpoint40pre8 (2001/09/05)
4933  o new package rw/  o new package rw/
4934    Added method for dumping intermediate local arrays:    Added method for dumping intermediate local arrays:
4935    mdsio_writetile - same as mdsio_writefield except works from inside    mdsio_writetile - same as mdsio_writefield except works from inside
# Line 3721  o TAMC-related update to cope with mom_f Line 4948  o TAMC-related update to cope with mom_f
4948    currently nothing implemented to switch this storing off    currently nothing implemented to switch this storing off
4949    in case fluxform is used since no CPP flag available).    in case fluxform is used since no CPP flag available).
4950    
4951  checkpoint40pre7  checkpoint40pre7 (2001/08/14)
4952  o bug fix in dynamics.F  o bug fix in dynamics.F
4953    calc_viscosity called before k=1,Nr loop.    calc_viscosity called before k=1,Nr loop.
4954  o added some #ifdef's ALLOW_PASSIVE_TRACER  o added some #ifdef's ALLOW_PASSIVE_TRACER
4955  o cleaned initialisations in ctrl_map_ini  o cleaned initialisations in ctrl_map_ini
4956    related to TAF    related to TAF
4957    
4958  checkpoint40pre6  checkpoint40pre6 (2001/08/13)
4959  o split dynamics into thermodynamics & dynamics  o split dynamics into thermodynamics & dynamics
4960  o corresponding split of calc_diffusivity into  o corresponding split of calc_diffusivity into
4961    calc_diffusivity, calc_viscosity    calc_diffusivity, calc_viscosity
# Line 3736  o corresponding split of calc_diffusivit Line 4963  o corresponding split of calc_diffusivit
4963  o Added diffkr, kapgm to control variables  o Added diffkr, kapgm to control variables
4964  o bug fix in gmredi_slope_limit for ldd97  o bug fix in gmredi_slope_limit for ldd97
4965    
4966  checkpoint40pre5  checkpoint40pre5 (2001/07/31)
4967  o proper initialization of Adams-Bashforth time stepping  o proper initialization of Adams-Bashforth time stepping
4968    + uses forward step for very first step of model (iter=0)    + uses forward step for very first step of model (iter=0)
4969  o re-generated *all* output since almost all output is modified by this  o re-generated *all* output since almost all output is modified by this
# Line 3750  o added new expt "solid-body.cs-32x32x1" Line 4977  o added new expt "solid-body.cs-32x32x1"
4977    + this uses an alternative form of ini_curvilinear_grid.F which    + this uses an alternative form of ini_curvilinear_grid.F which
4978      is not necessarily any better than the current one...      is not necessarily any better than the current one...
4979    
4980  checkpoint40pre4  checkpoint40pre4 (2001/07/30)
4981  o added re-initialisations of utrans,vtrans,rtrans in  o added re-initialisations of utrans,vtrans,rtrans in
4982    calc_common_factors which are crucial for TAF.    calc_common_factors which are crucial for TAF.
4983  o extended iMin,jMin range for calc_common_factors,  o extended iMin,jMin range for calc_common_factors,
# Line 3758  o extended iMin,jMin range for calc_comm Line 4985  o extended iMin,jMin range for calc_comm
4985  o added option ALLOW_PASSIVE_TRACER  o added option ALLOW_PASSIVE_TRACER
4986  o a few minor updates and fixes  o a few minor updates and fixes
4987    
4988  checkpoint40pre3  checkpoint40pre3 (2001/07/13)
4989  o created calc_gtr1.F for gad package  o created calc_gtr1.F for gad package
4990  o split the_main_loop and re-introduced forward_step  o split the_main_loop and re-introduced forward_step
4991  o some recomputations of nIter0 for TAMC  o some recomputations of nIter0 for TAMC
4992    
4993  checkpoint40pre2  checkpoint40pre2 (2001/07/13)
4994  o Updated to latest branch of AJA, JMC  o Updated to latest branch of AJA, JMC
4995  o Added gradient check package  o Added gradient check package
4996  o Added routines for passive tracer handling  o Added routines for passive tracer handling
4997  o Added carbon sequestration sensitivity experiment  o Added carbon sequestration sensitivity experiment
4998    
4999  checkpoint39  checkpoint39 (2001/05/14)
5000   o Modifications and fixes to support TAMC   o Modifications and fixes to support TAMC
5001     (mainly missing or wrong directives)     (mainly missing or wrong directives)
5002   o Corrected common blocks when fooling TAMC to produce adjoint I/O   o Corrected common blocks when fooling TAMC to produce adjoint I/O
# Line 3783  checkpoint39 Line 5010  checkpoint39
5010           (NB: this is not the full ECCO environment)           (NB: this is not the full ECCO environment)
5011   o disabled some packages by default in genmake   o disabled some packages by default in genmake
5012    
5013  checkpoint38  checkpoint38 (2001/04/10)
5014   o see notes_c37_adj.txt   o see notes_c37_adj.txt
5015   o corrected wrong layer index in external_forcing_t   o corrected wrong layer index in external_forcing_t
5016   o replaced the_main_loop/forward_step by the_main_loop   o replaced the_main_loop/forward_step by the_main_loop
# Line 3791  checkpoint38 Line 5018  checkpoint38
5018     (replaced criteria for initial/final state)     (replaced criteria for initial/final state)
5019   o added runtime flag for pre-C35 pickups: usePickupBeforeC35   o added runtime flag for pre-C35 pickups: usePickupBeforeC35
5020    
5021  checkpoint37  checkpoint37 (2001/03/13)
5022   o mdsio.F routine split and packaged in pkg/mdsio   o mdsio.F routine split and packaged in pkg/mdsio
5023     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
5024      used unless genmake -disable=mdsio)      used unless genmake -disable=mdsio)
# Line 3808  checkpoint37 Line 5035  checkpoint37
5035   o Non-Hydrostatic pickup file Pb fixed.   o Non-Hydrostatic pickup file Pb fixed.
5036   o bug with Rigid-lid version (since c35) fixed.     o bug with Rigid-lid version (since c35) fixed.  
5037    
5038  checkpoint36  checkpoint36 (2001/02/20)
5039   o implement Crank-Nickelson barotropic time-stepping   o implement Crank-Nickelson barotropic time-stepping
5040   o recover Time-Average diagnostics   o recover Time-Average diagnostics
5041   o fix Pb in checkpoint (PR#19)   o fix Pb in checkpoint (PR#19)
5042   o AIM become a standard package ; clean unused CPP_kees   o AIM become a standard package ; clean unused CPP_kees
5043    
5044  checkpoint35  checkpoint35 (2001/02/08)
5045   o subtantial rewrite of dynamics.f   o subtantial rewrite of dynamics.f
5046   o allows staggered time-stepping   o allows staggered time-stepping
5047   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
5048   o added bottom drag (linear + quadratic)   o added bottom drag (linear + quadratic)
5049    
5050  checkpoint34  checkpoint34 (2001/01/30)
5051   o Modified exchange routines for correct reverse simulation.   o Modified exchange routines for correct reverse simulation.
5052   o Added verification output to comply with bug fix in impldiff.F   o Added verification output to comply with bug fix in impldiff.F
5053     as of c33 (exp2, natl_box).     as of c33 (exp2, natl_box).
# Line 3831  checkpoint34 Line 5058  checkpoint34
5058   o Added routine GLOBAL_SUM_INT to global_sum.F   o Added routine GLOBAL_SUM_INT to global_sum.F
5059   o Added mdsio_gl.F for ECCO purposes.   o Added mdsio_gl.F for ECCO purposes.
5060    
5061  checkpoint33  checkpoint33 (2000/11/30)
5062   o Fixed bug in lower BC in impldiff.F   o Fixed bug in lower BC in impldiff.F
5063   o Fixed confusion about units of forcing arrays in FFIELDS.h   o Fixed confusion about units of forcing arrays in FFIELDS.h
5064     namely Fu,Fv,Qnet,Qsw,EmPmR:     namely Fu,Fv,Qnet,Qsw,EmPmR:
# Line 3849  checkpoint33 Line 5076  checkpoint33
5076       possibly use them.       possibly use them.
5077   o Corrected genmake to delete a temporary file during configuration   o Corrected genmake to delete a temporary file during configuration
5078    
5079  checkpoint32  checkpoint32 (2000/11/13)
5080   o Scaling of forcing fields moved from external_forcing.F to   o Scaling of forcing fields moved from external_forcing.F to
5081     external_fields_scale.F, called directly after loading fields.     external_fields_scale.F, called directly after loading fields.
5082   o Surface relaxation terms added to surface tendency fields in   o Surface relaxation terms added to surface tendency fields in
# Line 3860  checkpoint32 Line 5087  checkpoint32
5087   o Modifications and bug fixes in KPP package.   o Modifications and bug fixes in KPP package.
5088   o Verification experiment for KPP added (verification/nat_box/)   o Verification experiment for KPP added (verification/nat_box/)
5089    
5090  checkpoint31  checkpoint31 (2000/09/11)
5091   o Packages interface brought in line with defined standard   o Packages interface brought in line with defined standard
5092     -> new routines packages_...F     -> new routines packages_...F
5093     -> changes in initialise_fixed.F, initialise_varia.F     -> changes in initialise_fixed.F, initialise_varia.F
# Line 3877  checkpoint31 Line 5104  checkpoint31
5104     - not yet tested for GMRedi.     - not yet tested for GMRedi.
5105     - not yet tested for KPP.     - not yet tested for KPP.
5106    
5107  checkpoint30  checkpoint30 (2000/07/13)
5108   o Updates for OBCs   o Updates for OBCs
5109   o New experiment for test OBCs (internal_wave)   o New experiment for test OBCs (internal_wave)
5110   o New output.txt in verification/exp4/results/   o New output.txt in verification/exp4/results/
# Line 3886  checkpoint30 Line 5113  checkpoint30
5113   o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)   o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
5114     and entry for T90 in genmake     and entry for T90 in genmake
5115    
5116  checkpoint29  checkpoint29 (2000/06/21)
5117   o packaged KPP and GM/Redi   o packaged KPP and GM/Redi
5118    
5119  checkpoint28  checkpoint28 (2000/06/09)
5120   o Corrected initialization of hFacMin for difference vertical coordinates   o Corrected initialization of hFacMin for difference vertical coordinates
5121   o Modified calculation of partial cell thickness to more robust algorithm   o Modified calculation of partial cell thickness to more robust algorithm
5122   o config_summary.F: replaced write_1D_... by write_0D_...   o config_summary.F: replaced write_1D_... by write_0D_...
# Line 3902  checkpoint28 Line 5129  checkpoint28
5129     included store directives and tape key computations required for TAMC.     included store directives and tape key computations required for TAMC.
5130   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
5131    
5132  checkpoint27  checkpoint27 (2000/04/10)
5133   o fixed calc_isoslopes() to so that cancellation of terms in tensor   o fixed calc_isoslopes() to so that cancellation of terms in tensor
5134     formulation works properly with variable resolution.     formulation works properly with variable resolution.
5135   o restructured the calling tree between the_model_main() and dynamics()   o restructured the calling tree between the_model_main() and dynamics()
# Line 3910  checkpoint27 Line 5137  checkpoint27
5137   o introduced initialization file pSurfInitFile for free surface (cg2d_x)   o introduced initialization file pSurfInitFile for free surface (cg2d_x)
5138     in new routine ini_psurf()     in new routine ini_psurf()
5139    
5140  checkpoint26  checkpoint26 (2000/04/05)
5141   o moved some #ifdef in optional routines to encompass everything   o moved some #ifdef in optional routines to encompass everything
5142     except the argument declarations. This was using up some memory.     except the argument declarations. This was using up some memory.
5143   o fixed macros like _ADT to work with both versions of Linux cpp   o fixed macros like _ADT to work with both versions of Linux cpp
# Line 3920  checkpoint26 Line 5147  checkpoint26
5147     (macros are now in eesupp/inc/CPP_EEMACROS.h)     (macros are now in eesupp/inc/CPP_EEMACROS.h)
5148   o patch for 2 processor JAM mode   o patch for 2 processor JAM mode
5149    
5150  checkpoint25  checkpoint25 (2000/03/15)
5151   o updates for OBCs and NH   o updates for OBCs and NH
5152   o dramatically reduced memory usage   o dramatically reduced memory usage
5153   o added "JAM" routines for use on Artic network   o added "JAM" routines for use on Artic network
# Line 3931  checkpoint25 Line 5158  checkpoint25
5158      an explicit free-surface option)      an explicit free-surface option)
5159   o initial state input files for U and V   o initial state input files for U and V
5160    
5161  checkpoint24  checkpoint24 (1999/08/02)
5162   o Removed some spurious "REAL"s   o Removed some spurious "REAL"s
5163   o Updated KPP to latest version from JPL   o Updated KPP to latest version from JPL
5164   o Added a COS(latitude) in horizontal viscosity   o Added a COS(latitude) in horizontal viscosity
5165    
5166  checkpoint23  checkpoint23 (1999/05/26)
5167   o Added del^4 diffusion for salt and temperature   o Added del^4 diffusion for salt and temperature
5168   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
5169    
5170  checkpoint22  checkpoint22 (1999/05/18)
5171   o Made many small changes: implicit none, format(i5), etc...   o Made many small changes: implicit none, format(i5), etc...
5172   o Introduced KPP mixing scheme (compiles and runs but *not* tested)   o Introduced KPP mixing scheme (compiles and runs but *not* tested)
5173    
5174  checkpoint21  checkpoint21 (1999/05/18)
5175   o Introduced new I/O package that supports direct-access records (mdsio.F)   o Introduced new I/O package that supports direct-access records (mdsio.F)
5176   o Split-up mid-level I/O routines   o Split-up mid-level I/O routines
5177   o Updated input data for experiments 0,1,2,4 and 5   o Updated input data for experiments 0,1,2,4 and 5
5178   o Finally removed the genmake.* scripts (everyone seems happy with genmake)   o Finally removed the genmake.* scripts (everyone seems happy with genmake)
5179    
5180  checkpoint20  checkpoint20 (1999/03/22)
5181   o Tidied up open-boundaries some more   o Tidied up open-boundaries some more
5182   o Added non-hydrostatic code   o Added non-hydrostatic code
5183   o Fixed some input data   o Fixed some input data
5184   o Modified MPI start-up to work in "coupled" context.   o Modified MPI start-up to work in "coupled" context.
5185    
5186  checkpoint19  checkpoint19 (1998/12/15)
5187   o Tidied up directory structure for verification experiments.   o Tidied up directory structure for verification experiments.
5188   o Added new code for open boundaries.   o Added new code for open boundaries.
5189   o Corrected advective terms near boundaries.   o Corrected advective terms near boundaries.
# Line 3964  checkpoint19 Line 5191  checkpoint19
5191   o Implemented free-slip/no-slip BCs and del^4 dissipation.   o Implemented free-slip/no-slip BCs and del^4 dissipation.
5192   o Split default parameters out of ini_parms.F into set_defaults.F.   o Split default parameters out of ini_parms.F into set_defaults.F.
5193    
5194  checkpoint18  checkpoint18 (1998/11/30)
5195   o Further changes for optional code generation with   o Further changes for optional code generation with
5196     CPP - ugh!     CPP - ugh!
5197    
5198  checkpoint17  checkpoint17 (1998/11/03)
5199   o Beginning to incorporating modularity   o Beginning to incorporating modularity
5200     for supporting atmos. and ocean configs.     for supporting atmos. and ocean configs.
5201   o Small changes for TAMC complinace   o Small changes for TAMC complinace
5202   o New ultra simple test case. Barotropic box   o New ultra simple test case. Barotropic box
5203     configuration "exp0".     configuration "exp0".
5204    
5205  checkpoint16  checkpoint16 (1998/10/28)
5206   o Minor changes to exchange routines to support   o Minor changes to exchange routines to support
5207     accumulation in reverse mode. Adjoint of an     accumulation in reverse mode. Adjoint of an
5208     assignment is an addition.     assignment is an addition.
# Line 3983  checkpoint16 Line 5210  checkpoint16
5210     syntax) and by g77 under Linux ( 72 character     syntax) and by g77 under Linux ( 72 character
5211     limit ).     limit ).
5212    
5213  checkpoint15  checkpoint15 (1998/09/29)
5214   Rewrote exchange routines to allow   Rewrote exchange routines to allow
5215   o General tile <-> tile connectivity.   o General tile <-> tile connectivity.
5216   o TAMC reverse mode flag ( is this really needed? )   o TAMC reverse mode flag ( is this really needed? )
# Line 3992  checkpoint15 Line 5219  checkpoint15
5219     shmput/shmget, VIA, SYSV shmem and every other cool     shmput/shmget, VIA, SYSV shmem and every other cool
5220     communication method.     communication method.
5221    
5222  checkpoint14  checkpoint14 (1998/09/09)
5223   Consistent isomorphism chages made. These allow dynamical core   Consistent isomorphism chages made. These allow dynamical core
5224   to support both pressure and meters as a vertical coordinate.   to support both pressure and meters as a vertical coordinate.
5225    
5226  checkpoint13  checkpoint13 (1998/07/17)
5227   Release which corrects global_max problem and a couple   Release which corrects global_max problem and a couple
5228   of KGM time-averaging diagnostic errors. Also contains   of KGM time-averaging diagnostic errors. Also contains
5229   a double-gyre experiment setup as well as the baseline   a double-gyre experiment setup as well as the baseline
# Line 4011  branch-point-rdot Line 5238  branch-point-rdot
5238   I don't want to commit the rDot to the main-trunk until   I don't want to commit the rDot to the main-trunk until
5239   we've actually tested it...   we've actually tested it...
5240    
5241  checkpoint12  checkpoint12 (1998/07/08)
5242   Tidy up and added generic genmake script (formerly   Tidy up and added generic genmake script (formerly
5243   configure script).   configure script).
5244   Released to testers.   Released to testers.
5245    
5246  checkpoint11  checkpoint11 (1998/07/02)
5247   Re-arranged initialise() and introduced ini_vertical_grid()   Re-arranged initialise() and introduced ini_vertical_grid()
5248   and ini_masks_etc().   and ini_masks_etc().
5249    
5250  checkpoint10  checkpoint10 (1998/07/01)
5251   Introduced the configure script.   Introduced the configure script.
5252   Separated out the diags package.   Separated out the diags package.
5253   Added template for writing time-averages of tile/intermediate quantities.   Added template for writing time-averages of tile/intermediate quantities.
5254   Updated SIZE.h in exp2 and made the data big-endian.   Updated SIZE.h in exp2 and made the data big-endian.
5255    
5256  checkpoint9  checkpoint9 (1998/06/22)
5257   MPI fix. Filename changes (meta/data). salbin*y stuff.   MPI fix. Filename changes (meta/data). salbin*y stuff.
5258   General tidy-up.   General tidy-up.
5259   SST.bin SSS.bin added to verification/exp2   SST.bin SSS.bin added to verification/exp2
5260    
5261  checkpoint8  checkpoint8 (1998/06/22)
5262   Inludes time-dependant forcing and time-averaging.   Inludes time-dependant forcing and time-averaging.
5263   Works at 4x4 and 2.8125x2.8125 global   Works at 4x4 and 2.8125x2.8125 global
5264    
# Line 4041  checkpoint7-4degree-ref Line 5268  checkpoint7-4degree-ref
5268   model etc..   model etc..
5269   Configured for verification/exp2 - 4 degree global, two process.   Configured for verification/exp2 - 4 degree global, two process.
5270    
5271  checkpoint7  checkpoint7 (1998/06/15)
5272   Created by cnh   Created by cnh
5273   Simple 4 degree global simulation   Simple 4 degree global simulation
5274   configuration.   configuration.
# Line 4049  checkpoint7 Line 5276  checkpoint7
5276   hydrography, bathymetry etc   hydrography, bathymetry etc
5277   Does not include Heat Flux and E-P   Does not include Heat Flux and E-P
5278    
5279  checkpoint6  checkpoint6 (1998/06/08)
5280   Created by cnh   Created by cnh
5281   merged checkpoint5 with CD and   merged checkpoint5 with CD and
5282   spherical polar code.   spherical polar code.
5283   Still some problems with GM Redi   Still some problems with GM Redi
5284   abd full topography.   abd full topography.
5285    
5286  checkpoint5  checkpoint5 (1998/06/08)
5287   Created by AJA   Created by AJA
5288   contains updates to GM Redi   contains updates to GM Redi
5289   and reordered timestepping loop   and reordered timestepping loop
5290   for Implicit Diffusion.   for Implicit Diffusion.
5291    
5292  checkpoint4  checkpoint4 (1998/05/30)
5293   Created by cnh   Created by cnh
5294   Contains memory saving macros ( _rdxc etc..) for when   Contains memory saving macros ( _rdxc etc..) for when
5295   grid variations are limited.   grid variations are limited.
5296   Contains polynomial coeffs for EOS and knudsen program   Contains polynomial coeffs for EOS and knudsen program
5297   for generation.   for generation.
5298    
5299  checkpoint3  checkpoint3 (1998/05/26)
5300   Created by cnh   Created by cnh
5301   Added extra flags for runtime options   Added extra flags for runtime options
5302   Added this file   Added this file

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