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revision 1.127 by adcroft, Thu Jan 30 18:35:42 2003 UTC revision 1.342 by edhill, Wed Sep 8 18:02:29 2004 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    o add version info (via BUILD_INFO.h) to MNC and stdout
7    
8    checkpoint54e_post
9    o add two new packages
10      - pp81 (Packanowski and Philander, 1981), Richardson number and
11        stratification dependent mixing
12      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
13      - these scheme operate in a similar manner as KPP (without ghat, of
14        course), however there is only one diffusivity that is used for both
15        temperature and salinity (and passive tracers)ç
16    o add offline package
17    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
18      provided by Stephanie Dutkiewicz
19    o genmake2: add ability to search for C compilers and cleanup test output
20      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
21    
22    checkpoint54d_post
23    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
24    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
25      leading to additional shift by 5 days each year of integration
26       (i.e. leading to considerable offset over the years)
27    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
28    o start with no AB and no initial filtering (staggerTimeStep):
29      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
30    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
31      (external loading & cpl import/export stay in forward_step.F)
32    o update coupling interface to work with new staggerTimeStep
33    o change MDSIO ptracers_pickup.
34    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
35    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
36    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
37    
38    checkpoint54c_post
39    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
40      this affects (truncation error) output.txt of test-exp:
41       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
42    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
43    o change Qnet to always be the net heat flux, (+upward).
44      affects (truncation error) output of natl_box exp.: updated
45    o define the max number of passive tracers in PTRACERS_SIZE.h
46    o start to test mnc routinely in exp0
47    o add sea-ice loading (sIceLoad) as a new forcing field.
48    
49    checkpoint54b_post
50    o add testreport "-j JOBS" option for parallel builds (tested and pretty
51       impressive on Altix and Opteron systems)
52    o diagnostics can now write NetCDF files through the mnc package
53    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
54    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
55    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
56      affects (truncation error) output of lab_sea & natl_box exp.: updated
57    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
58    
59    checkpoint54a_post
60    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
61    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
62    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
63    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
64      + internal_wave (shift in writing cg2d_ini_res)
65    checkpoint54a_pre
66    
67    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
68      - modified verification/lab_sea and natl_box_adjoint accordingly
69    
70    checkpoint54
71    checkpoint53g_post
72    o prepare splitting of thermodynamics: store convect.counter in common block
73    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
74      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
75    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
76    o new parameter "nShapS": allow to treat differently S from T (nShapT)
77    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
78    o restore adjointability
79    
80    checkpoint53f_post
81    o modifications that affect AIM experiment results (update output.txt):
82      - no advection of S at top interface Nr (pkg/generic_advdiff)
83      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
84    o AIM pkg:
85      - include stability function into surf.Flux derivative relative to Tsurf
86      - calculate clear-sky radiation & surface temp. change (for diagnostics)
87    
88    checkpoint53e_post
89    o merged cylindrical coord configuration
90    o added rotating_tank experiment
91    checkpoint53e_pre
92    
93    checkpoint53d_post
94    o faulks upgraded: re-generate output.txt that have changed:
95       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
96    o Added Bryan and Lewis, 1979, vertical diffusivity profile
97    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
98    o added Sadourny discretization of Coriolis
99      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
100      - re-enabled use of omega3 (useAbsVorticity)
101    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
102      vector-invariant equations
103      - note: does *NOT* yet use same variable visc. for no-slip BC's.
104    o recoded the lateral boundary conditions for non-hydrostatic w, this time
105      hopefully without new bugs
106      - still to do: biharmonic friction for non-hydrostatic w
107    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
108    o regenerated output for global_ocean_ebm (using -ieee)
109    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
110      of mom_common/
111      - simple re-arrangement of instructions within computing loop
112    checkpoint53d_pre
113    
114    checkpoint53c_post
115    o new version of coupler for AIM+thSIce and Ocean models
116     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
117     - land: change Evaporation of snow
118     - aim with thSIce: fix bug in snow-precip.
119    o changes to calc_gw.F
120     - bug fix for w^2 term near the bottom boundary
121     - (hopefully) improve the lateral slip boundary condtions for use with
122        partial/looped cells
123      - because the bug fix changes two verification experiments anyway (exp5
124        and plume on slope), change the lateral boundary condition from half slip
125        to the value of no_slip_sides
126    o ebm package wasnt quite up to the parallel task. Fixed that.
127    o Adjoint of EBM package + verification
128      * TLM OK
129      * ADM not sufficient accuracy yet (needs further testing)
130    
131    checkpoint53b_post
132    o Commiting new energy balance model to repository
133      * package is pkg/ebm
134      * verif. is verification/global_ocean_ebm
135      * references are in ebm_driver.F
136    C      * X. Wang, P. Stone and J. Marotzke, 1999:
137    C        Global thermohaline circulation. Part I:
138    C        Sensitivity to atmospheric moisture transport.
139    C        J. Climate 12(1), 71-82
140    C      * X. Wang, P. Stone and J. Marotzke, 1999:
141    C        Global thermohaline circulation. Part II:
142    C        Sensitivity with interactive transport.
143    C        J. Climate 12(1), 83-91
144    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
145    C        Destabilization of the thermohaline circulation
146    C        by atmospheric eddy transports.
147    C        J. Climate 7(12), 1870-1882
148    o Will need long integration testing.
149    checkpoint53b_pre
150    
151    o created pkg/mom_common in preparation for variable viscosity code
152    o renamed and split ini_mnc_io
153    o pkg/land: only liquid water can diffuse or run-off
154    o AIM using land: soil wetness availability account for snow
155    o added printMapIncludesZeros to EEPARMS namelist
156    
157    checkpoint53a_post
158    o restore TAMC compatiility for exf_constants.h
159      (no usage of _d in .h)
160    o Additional storing in KPP in an attempt to fix
161      TAMC problem with adjoint of KPP code.
162      (no success...)
163      Identical code works fine with TAF.
164    o Fixed verification/natl_box_adjoint experiments.
165      Initial conditions for Experiments 4 and 5 are now
166      set to "SEAICE_initialHEFF=0", which is more reasonable,
167      and hence gives results closer to that of Experiment 2.
168      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
169    
170    checkpoint53
171    o stable checkpoint with up to date adjoint
172      TLM tests only run for 1st grdchk at the moment. Its unclear if
173      this is a code problem or a problem with resetting code for g_
174      variables that is being autogenerated wrong.
175      Otherwise:
176       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
177       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
178         are both still in chaos following their security messes.
179    
180    checkpoint52n_post
181    o various build (mostly genmake2) changes including:
182      - ability to build/run more easily within Cygwin and MacOS X
183      - more complicated Makefiles with a stronger dependence on Gnu Make
184    o pkg/seaice modifications
185      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
186        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
187        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
188      - changed proxy for geostrophic velocity and updated
189        verification/lab_sea/results/* accordingly
190      - removed ADI dynamic solver from pkg/seaice
191      - replaced all occurrences of 1/CSTICE or 1/CSUICE
192        they caused a segmentation fault under certain circumstances
193      - removed unused field WATR
194    o bug fix in exf-package:
195      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
196         now reflect that.
197    o small fixes in the cal-package:
198      - set reference date to first of January for the 'model'-calendar
199      - failing of cal_CheckDate in cal_FullDate now actually results in a
200        warning
201    o small modifications in exf-package to increase flexibility:
202      - change climtempfreeze from a constant to a runtime parameter that
203        is specified in data.exf_clim (default = -1.9)
204      - introduce runtime parameter windstressmax (default = 2.0) that is
205        specified in data.exf
206    o fix in pkg/thsice:
207      - update Evap (Tsf changes) to be consistent with Latent heat flux
208      - maintain snow precipitation unchanged (even if Tsf >=0).
209     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
210    
211    checkpoint52m_post
212    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
213      this does not change any of the results, because myIter=0 in swfrac always
214      lead to jwtype=2 (the default anyway), but the call makes little sense
215      as a default
216    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
217    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
218      atmospheric model (AIM) to use it ; add a "slab ocean" component.
219    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
220    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
221    o extending useSingleCpuIO option to work with new exch2 I/O format
222      - old-style, missing-tile I/O is still accessible by defining CPP
223        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
224    o monitor package can write to NetCDF files and/or STDOUT
225    o fix re-definition bug in MNC_GRID_INIT_ALL()
226    o doc/api_reference added
227      - a framework for building an API Reference Manual using all
228        the "protex" comments embedded in the code
229      - see pkg/generic_advdiff, pkg/mnc for examples
230    o MNC:
231      - make myThid the last argument for all subroutines
232      - new default for the grid files: NO halos
233      - add useMNC and other run-time flags
234      - separate per-file-group handling of the unlimited dimension
235      - early initialization of MNC w/ flags read at the eeboot stage
236        and lookup tables set in initialize_fixed
237      - write all MNC output to a freshly-created directory
238    o thermodynamics sea-ice (thsice) is now tested with testreport.
239    o test exp. advect_cs: use the standard cs32 grid ; update output.
240    o Added functionality to grdchk:
241      pick global i,j,k position (or nearest wet) where to perform check.
242    
243    checkpoint52l_post
244    o new land formulation:
245      a) use ground enthalpy as prognostic variable to ensure exact
246         energy conservation.
247      b) account for water temperature and for latent heat of freezing
248         in all processes (rain, run-off, ground storage)
249      c) compute surface and ground temperature implicitly.
250    o aim_v23 modification for new land model:
251      a) Treat separately land / ocean / sea-ice surface fluxes
252         to allow implicit computation of land & sea-ice surface temp.
253      b) add snow precipitation.
254    checkpoint52l_pre
255    
256    o fix problem (when 1 tile is empty) in min/max monitor.
257    o fix bug in timeAve (u,vZetatave in common block)
258    o no restoring terms under ice for pkg/seaice
259    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
260    o bug fix for pkg/seaice pickups
261    o change MNC call locations and add coordinate attributes
262    o mask vorticity at the corner ; affects global_ocean.cs output
263    o fix ini_curvilinear_grid ; test CS experiments with mpi
264    o aim.5l_cs: modify sea-ice fraction input file ; update output
265    o exf: Adding simple range check routine for exf fields after read
266    
267    checkpoint52k_post
268    o removed top-level directory "diags"
269      - we migrated these functions to pkg/timeave a long time ago
270    o fixed bug introduced in pkg/monitor
271    o accuracy ctrlprec = 32 insuffient for gradient checks using
272      averaged fields (I/O via cost_averages)
273      -> use ctrl.h in active_file*.F to control I/O precision.
274    o paramter list of CALL ADTHE_MAIN_LOOP
275    o added initial do_the_model_io to ecco
276    o set all ...Freq to zero after cost_final
277      taveFreq, dumpFreq, pChkptFreq
278    o MAIN and ECCO differentiability restored
279    
280    checkpoint52j_post
281    o fix nchklev in tamc.h for global_ocean...
282    o Bringing flow and store directives up-to-date
283    o Really weird thing!
284      call do_the_model_io from the_main_loop with parameters
285      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
286      TAF places a faulty re-call of initialise_varia
287      after cost_final call which should not be there!
288    checkpoint52j_pre
289    
290    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
291      error messages
292    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
293    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
294      debug output
295    o modfied mdsio_writefield.F to handle non-global files under exch2
296    o update AIM Cubed-Sphere exp (aim.5l_cs):
297      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
298    o update AIM Equatorial Channel exp:
299      use standard aim_v23 pkg and change the SST fields to be more realistic.
300    o globalFile now works with exch2
301    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
302      mon_vort3.F to make exch2 friendly with >1 tile per cube face
303    o limit timeave output for hi-res integrations
304    
305    checkpoint52i_post
306    o removed CPP_EEOPTIONS.h from verification/*/code
307    o updated the tiling for global_ocean_pressure
308    checkpoint52i_pre
309    
310    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
311      the old pkg/aim).
312    
313    checkpoint52h_pre
314    o shortened offending lines in exch2_send_rx?.template
315    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
316    o genmake2: add build & execute test for NetCDF code
317    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
318      old grid files, moved CPP_EEMACROS.h to pkg/exch2
319    o added useSingleCPUIO flag to monitor.F and mon_out.F
320    o added temporary hack for sea-ice dynamics on the cube:
321      metric terms are ignored and it is assumed that
322      there is no sea-ice on cube faces 1, 2, 4, and 5.
323    
324    checkpoint52f_post
325    o added exch2 cube routines to pkg/exch2
326    o modified hs94.cs-32x32x5 to use it
327    o added new grid files to hs94.cs-32x32x5
328    checkpoint52f_pre
329    
330    checkpoint52e_post
331    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
332      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
333    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
334      to work with implicit vertical advection and AB ;
335    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
336    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
337     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
338    checkpoint52e_pre
339    
340    o fix bug in impldiff when Nr=1 or Nr=2.
341    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
342    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
343    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
344      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
345    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
346    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
347    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
348    
349    checkpoint52d_post
350    o re-tiled many expts to allow comparison in multi-processor mode
351      - updated output accordingly
352      - changed hs94.128x64x5 to use intial T from file rather than use the
353        random number generator
354    o add infrastructure in model routines for fizhi and gridalt packages
355    o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
356    o changes to permit hi-res, cubed-sphere, configuration
357      - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
358      - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
359      - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
360        of surface winds for the cube
361      (A verification experiment, based on global_ocean.cs32x15, but with
362       pkg/seaice turned on and with on-the-fly interpolation from the NCEP
363       Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
364       complete with example surface forcing files and matlab scripts to look
365       at the output and compare it with that of global_ocean.cs32x15.)
366    o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
367       but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
368       to conform to the common rule.
369    o check-in the first version of the coupler + interfaces for multi-components
370       set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
371       - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
372       - atmosphere: use pkg aim_v23 ; no sea-ice for now.
373       - ocean and atmos. share the same horizontal grid (no interpolation).
374       - exchanges between component and coupler is done in forward_step
375    o new verification experiment, cpl_aim+ocn:
376       coupled ocean - AIM atmosphere on cs32 grid.
377    
378    checkpoint52d_pre
379    o surface flux time-av diagnostic modified for NLFS & RealFreshWater
380    o add call to AIM pendant S/R in external_forcing & external_fields_load.F
381    
382    checkpoint52c_post
383    o Fixing OPTIONS files for use of exf:
384      - ALLOW_ECCO not needed
385      - ECCO_CPPOPTIONS.h should not be included from
386        EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
387        as has been the case in the past
388      - All cal/exf related options are currently set in
389        single header file. Should remain so until we
390        agree on a consistent new policy.
391    o Removed all CPP options for cal package.
392      cal has no more CPP options.
393    o modified STOREs in GAD_ADVECTION
394    o corrected key comp. for passkey
395    
396    checkpoint52b_post
397    o new version: "thsice" of thermodynamic sea-ice pkg:
398     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
399     - modify fluxes but do not change theta directly;
400     - light cleaning of bulk_force pkg (still needed with thsice).
401     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
402       + output_thsice.txt to test thsice & bulk_force pkgs.
403    o put back grid & coriolis monitor output.
404    checkpoint52b_pre
405    
406    o call "do_the_model_io" at the beginning (=> dump initial state)
407    o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
408    o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
409      (need info on NUMBER_OF_PTRACERS)
410    o missing PTRACERS headers in some routines
411    o default tamc.h in pkg/autodiff supposed to crash
412      to ensure proper customization
413    
414    checkpoint52a_post
415    o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
416      - moved surfaceTendencyTice from pkg/seaice to main code
417      - subroutine FREEZE_SURFACE now limits only surface temperature
418        and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
419        => new output.txt for global_ocean.cs32x15 & global_with_exf
420      - keep the old version of FREEZE for backward compatibility;
421        global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
422      - corresponding modifs for TAF directives
423    o added surface flux output variables to TIMEAVE_STATVARS
424    o time-averaged output for pkg/ptracers
425    o fix problem with ECCO-related divided adjoint
426      snapshot file was missing some ad-variables,
427      but no warning issued by TAF
428    
429    checkpoint52a_pre
430    o some bug fixes for #undef REAL4_IS_SLOW
431    
432    checkpoint52 = ecco_c52_e35
433    o after testing adjoints of checkpoint51u_post
434    
435    checkpoint51u_post
436    o this is the post-merge tag of the ecco-branch
437      (needs another clean checkout and re-testing)
438    o various natl_box_adjoint configs and results
439      but no input fields
440    o obcs adjoint not yet merged!
441    o adding ECCO global 1x1 and 2x2 degree configs
442    o updated/extended some store directives for seaice
443    o pkg/ecco now containes ecco-specific part of cost function
444    o top level routines the_main_loop, forward_step
445      supersede those in model/src/
446      previous input data.cost now in data.ecco
447      (new namelist ecco_cost_nml)
448    o in ctrl/ cleaned some cross-dependencies and updated CPP options
449    
450    checkpoint51t_post
451    o this is the pre-merge tag of the ecco-branch
452    
453    checkpoint51s_post
454    o cleanup: removed various obsolete #define-s
455    o pkg/grdchk
456      - renamed 'ph-grd 3' to 'grad-res'
457      - merged from ecco-branch
458        (remaining bug fixes for obcs gradient checks)
459      - additional high-precision output for testreport
460        (grep for 'precision_grdchk_result')
461    
462    checkpoint51r_post
463    o cleaned up or removed CPP_OPTIONS.h files
464    o updated results for some of the tests to reflect the new
465      optfiles (-ieee: -O0 instead of -O3)
466    
467    checkpoint51q_post
468    o cd_code:
469      - moved cd_scheme.F -> cd_code_scheme.F
470      - separate read_checkpoint from cd_code_ini_vars.F
471      - separated cd_code part from write_checkpoint
472      - updated AD_SOURCE, generated .flow
473      - added CD_CODE_VARS.h to the_main_loop
474      - Moving cd_code specific store dir.s to pkg/cd_code
475    o ctrl package totally restructured
476      - pack/unpack now optional and decoupled from
477        xx_/adxx_ I/O
478      - ctrl_pack/unpack cleaned
479        (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
480      - confined inclusion of AD_CONFIG.h to where necessary.
481    o genmake2: changed AD dependencies from SRCFILES to AD_FILES
482    
483    checkpoint51p_post
484    o create initial cd_code package
485      - WARNING: the initialization of fields within packages
486        is broken because INI_FIELDS (where READ_CHECKPOINT is
487        called) is called *before* PACKAGES_INIT_VARIABLES.
488        This seems to be backwards since
489        1) its important to initially zero the entire field including
490           the "halo" region
491        2) zeroing needs to be done *before* reading pickup info
492           and the pickup call might or might not happen in any
493           particular run
494      - this needs an overhaul for R2
495    o cleanup verification/*/code/GMREDI_OPTIONS.h
496    o cleanup testreport
497    
498    checkpoint51o_post
499    o bringing AD-related verif's up to date with genmake2
500      - carbon/
501      - global_ocean.90x40x15/
502      - hs.94.1x64x5/
503      - (front_relax/ )
504    o (more) consistent directory structure for AD-related verif.'s
505    o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
506    o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
507    o bug fix in find_alpha.F for MDJWF:
508      - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
509        change rho -> rho-rhoConst
510      - replace call find_rho to find_rhonum
511    o initialisation of rFlx extended to full array (required by TAF)
512      and shifted to thermodynamics
513    o removed PTRACERS.h in ptracers routine
514    o added surfacetendencyPtr to S/R parameter list pracers_forcing
515    o Correcting initialisations for fVerU, fVerV.
516    o helping TAF to recognize dependency on kUp for
517      fVerU, fVerV
518    o Replacing delZ by delR in pkg/ctrl/
519    checkpoint51o_pre
520    
521    o undid all of cp51 pending some cleanups and discussion
522    o added the [#include "AD_CONFIG.h"] statement to all files that need
523       it for adjoint/tl #defines
524     o re-worked the build logic in genmake2 to support AD_CONFIG.h
525     o removed tools/genmake since it no longer works
526    
527    checkpoint51n_post
528    o modifications to make FREEZE flux visible to pkg/kpp
529      - moved surfaceTendencyTice from pkg/seaice to main code
530      - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
531      - subroutine FREEZE now limits only surface temperature
532        (this means new output.txt for global_ocean.90x40x15,
533         global_ocean.cs32x15, and global_with_exf)
534    o added surface flux output variables to TIMEAVE_STATVARS
535    
536    checkpoint51n_pre
537    o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
538    o added [#include "AD_CONFIG.h"] to all files that use the following
539      defines:
540      - ALLOW_ADJOINT_RUN
541      - ALLOW_TANGENTLINEAR_RUN
542      - ALLOW_ECCO_OPTIMIZATION
543    
544    checkpoint51m_post
545    o incorporating changes to get TAMC/TAF working in genmake2
546      - added new TAMC/TAF targets to the Makefile
547      - various cleanups related to package handling
548      - these changes should have no impact on the forward model
549    
550    checkpoint51l_post
551    o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
552     - faster algorithm for cal_addtime.F
553     - higher precision arithmetic, where needed
554     - pkg/exf *startdate variables changed from calendar date to
555       model integration time
556    
557    checkpoint51l_pre
558    o add salt flux to forcing fields (used when salty sea-ice forms or melts)
559    o enable to apply restoring on S & T only in a latitude band.
560    o update output (external_forcing_surf modif. change truncation errors)
561       global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
562    
563    checkpoint51k_post
564    o change default to: useNHMTerms=.FALSE.
565     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
566       adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
567     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
568        exp1, ideal_2D_oce
569     - change data file of oceanic exp (leave the results unchanged for now)
570       exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
571    o set gravitySign automatically according to the vertical coordinate used
572      (and change sign: back to "logical" value: +1 when R increases downward)
573    o added an include barrier to the default CPP_OPTIONS.h and
574      removed the #include "PACKAGES_CONFIG.h" from it
575    o fix a bug in mom_fluxform (from chk51j_post)
576    
577    checkpoint51j_post
578    o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
579    o adjusted some flow directives (dynamics, thermodynamics)
580    o added cubed-sphere case to test cost function
581    o heckpoint_lev?_directives.h now include
582      pkg-specific directives, whenever those are enabled.
583    o Moving pkg-specific flow directives to corresponding pkg
584      Moving pkg-specific differentiation list to corresponding pkg
585      Moving pkg-specific checkpoint-lev storing to corresponding pkg
586      ---> conventions are
587           - pkg_ad.flow
588           - pkg_ad_diff.list
589           - pkg_ad_check_lev?_dir.h
590    
591    checkpoint51i_post
592    o merge of the branch-genmake2
593      - knowingly breaks the older genmake
594      - automatic generation of all ALLOW_${PKG_NAME} defines
595      - new testreport supersedes older testscript
596    o large number of package inclusion and header cleanups
597    checkpoint51i_pre
598    
599    o new output for adjoin of global ocean vector invariant
600    o fix for checkpoint of thermodynamic seaice and bulk_force
601    o Steph gchem various cleanups
602    
603    checkpoint 51h_pre
604    o fixed some single quotes
605    o modify gchem pkg to be more versatile
606    o modifications to clean up dic pkg
607    o add pkg/cfc
608    
609    checkpoint51g_post
610    o provide links for ARPACK and ADM*TLM
611    o start removing verification/vero/
612    o update AD-related stuff
613      (in particular some IF-statements in model/src/ routines)
614    o adding to verification/global_ocean.90x40x15/ adjoint of
615      vector invariant setup
616    
617    checkpoint51f_post
618    o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
619    o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
620      of tracer Green's fucntions for ocean inversion project.
621    
622    checkpoint51f_pre
623    o Added on-the-fly spatial interpolation capability
624        "USE_EXF_INTERPOLATION" to pkg/exf.
625      - This is a temporary Cartesian-grid hack until
626        the super-duper ESMF coupler becomes available.
627      - See verification/global_with_exf/README for usage example.
628      - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
629        flags and modified pkg/seaice accordingly.
630    o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
631        and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
632        non-local transport term.
633    
634    checkpoint51e_post
635    o pkg/mom_vecinv:
636      - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
637      - add time-ave diagnostic of vorticity advection.
638    o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
639    o atmospheric geopotential: - include water vapor effect;
640                                - use p^kappa in p* scaling.
641    o land pkg: read initial state from files.
642    o AIM : add stratospheric drag in the upper level
643    
644    checkpoint51d_post
645    o change function ILNBLNK (=> last non-blank char.) to return zero
646      (instead of the string length) when the string. char is empty
647    o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
648    o modif's to restore TAMC compatibility
649      - avoid "_d" constructs in PARAMETER declarations
650      - avoid interrupting lines by comment lines
651    o Use cluster local disks for purely local I/O
652      vs. globally visible disks needed for ctrl stuff
653      (merged from ecco-branch)
654      - new active_file_loc... and mdsio_..._loc routines
655      - affected packages: autodiff, ctrl, grdchk, mdsio
656    
657    checkpoint51c_post
658    o introducing integer flag debugLevel
659      - debLevZero: suppress all output
660      - debLevA: standard
661      - debLevB: equivalent to current debugMode=.TRUE.
662    o introducing pathname variable mdsioLocalDir for mdsio
663      that can be specified at runtime
664      (relevant for cluster I/O to local disk)
665    `
666    >>>checkpoint51b_post
667    adjoint of ptracers
668    o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
669    o extended state in checkpoint_lev?, etc.
670    o alternative ctrl/cost with tr1 or ptracer
671    o new comlev1_bibj_ptracers
672    o new ptracers.flow
673    o made ptracers_forcing same as external_forcing_s
674    o added verification for adjoint with ptracers
675      - adm. grdchk fail so far
676      - tlm. grdchk OK
677      - checked tapelev/comlev recomputations: OK
678    <<<checkpoint51b_pre
679    
680    checkpoint51a_post
681    o added code for biogeochemistry package
682      - new pkgs: dic, gchem
683      - new subroutine in ptracers
684    o modify code for biogeo packages
685      - in model/src and pkg/ptracers
686    
687    checkpoint51
688    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
689      - autodiff, ctrl, exf, grdchk, seaice
690      kept separate packages
691      - cost, ecco, obcs
692    o updating verification/internal_wave, verification/lab_sea
693      (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
694    
695    checkpoint50i_post
696    o Preparing next differentiable checkpoint and sync
697      of MAIN vs. ecco-branch
698      - 1st step: this one is differentiable
699      - 2nd step: next(! not this) checkpoint will have updated packages
700                  from ecco-branch)
701    
702    checkpoint50h_post
703    o new package "land": provide surface BC for AIM.
704    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
705    o AIM: use true log-P extrapolation for near surface temp (= as in
706        F.Molteni paper) ; update aim.5l_cs output.
707    o New variable in PARM03 for more flexible pickups
708    o somewhat cleaned package initialisation sequence for
709      ctrl/ cost/ ecco/ in packages_... routines
710    
711    checkpoint50g_post
712    o merged with release1_p17 (pkg/seaice and verification/lab_sea)
713      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
714      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
715        made the default because of faster convergence than ADI
716    
717    checkpoint50f_post
718    o exf totally restructured
719      - replaced all exf_set_ routines by one generic exf_set_gen.F
720        and made sure it's still differentiable
721      - split exf_getffields.F into new exf_bulkformulae.F
722      - exf_inscal_/exf_outscal_ suffixes consistent with field names
723      - updated adjoint/makefile and relevant verif. accordingly
724    
725    checkpoint50f_pre
726     o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
727          + change Evap over land. (update aim.5l_cs output)
728     o added missing .cvsignores and made uniform across expts
729     o changed configuration of tidal_basin_2d expt
730     o added pkg/debug functions for tracing code in fatal crashes
731     o tidied pkg/monitor to use MONITOR_OPTIONS.h
732     o new fn in pkg/monitor to stop model if solution grows too big
733     o removed lots of single quotes from comments
734    
735    checkpoint50e_post
736    o make KPP work with PTRACERS
737     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
738       nearly a copy of kpp_transport_s
739     - there is no analogue to SurfaceTendencyS, so I have to use
740       gPtr(of the surface layer) instead
741    o add a new platform SunFire+mpi (SunFire 15000) to genmake
742    checkpoint50e_pre
743    
744    checkpoint50d_post
745    o change kpp output from multiple-record state files to single-record state
746      files analogous to write_state.F
747    o reduce the output frequency of cg3d-related stuff to the monitor frequency,
748      analogous to the cg2d-related output.
749    o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
750      so that writing to internal file fn (with length 512) fails.
751    checkpoint50d_pre
752    
753    checkpoint50c_post
754    o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
755    o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
756    o add time-average diagnostic of U*V and vertical diffusive flux for theta.
757    o bug fixed in convective adjustment diagnostic (multi-tile set-up).
758    o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
759    
760    checkpoint50c_pre
761    Merging from release1_p13:
762    o bug fix for pkg/seaice dynamic solver
763    o Added SEAICE_initialHEFF to pkg/seaice
764    
765    checkpoint50b_post
766    o store u*,v* in gU,V instead of in guNm1,gvNm1
767    o in order to put the momForcing out of the Adams-Bashforth:
768      move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
769      to timestep.F
770    o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
771    o re-generate output for highly sensitive test-exp:
772       global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
773    
774    checkpoint50b_pre
775    o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
776    o corrected CPP option mismatch in exf_Bulk... functions for case
777      #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
778    
779    checkpoint50a_post
780    o Bug fix for merging between c50 and KPP.
781      ikey was passed from thermodynamics to kpp_calc via
782      common block rather than being recomputed in kpp_calc,
783      in contradiction with new key itdkey.
784      New key ikppkey created, and tamc.h headers updated.
785    
786    checkpoint50
787    - 2nd step of merge with ecco-branch:
788      merge changes in ecco-branch back into main trunk
789    - bug fix in find_alpha
790    - more storing in gmredi_calc_tensor.F, kpp_routines.F
791    - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
792    - merged some sliced AD support routines
793    
794    checkpoint49
795    merged from ecco-branch:
796    o exf:
797      - Enable initialisation of forcing fields to constant
798        (runtime) values.
799      - in exf_getffields.F
800        Reduce i-/j-loop to interior domain, discarding overlaps.
801        That also fixes wrong TAF-key computations for key_1, key_2
802        with bulf formulae.
803      - exf_init.F modify #ifdef for exf_init_evap
804      - exf_getffieldrec.F, ctrl_getrec.F
805        The following INT-usages are not safe:
806          fldsecs  = int(fldsecs/fldperiod)*fldperiod
807          fldcount = int(fldsecs/fldperiod) + 1
808        and were modified.
809    o autodiff: checkpoint_lev...
810      - updated storing for bulk formulae (some arrays were missing)
811      - added state for seaice package
812      - synchronized with main branch
813    o DIVA:
814      Modif.s in
815      - the_main_loop.F
816      - the_model_main.F
817      and added cost_final_restore.F cost_final_store.F
818      o With these changes, it is possible to fully separate
819        the first forward run to compute the cost function (mdthe_main_loop)
820        and adjoint runs over individual DIVA intervals (adthe_main_loop)
821        into separate model executions.
822        This enables better tuning of DIVA to given queue sizes.
823      o Loss of cost function value in consecutive DIVA runs is
824        fixed by storing to 'costfinal' file.
825      o Appropriate call of ctrl_unpack/_pack,grdchk_main at
826        beginning/end of adjoint integration is accounted for.
827      The current changes apply to TAF-1.4.26.
828      TAF has one remaining bug, requiring one manual change
829      (see MITgcm manual).
830    o cal: synchronized between MAIN and ecco-branch
831    
832    checkpoint48i_post
833    o Changes to restore differentiability of code w.r.t. previous tag
834      (mostly adding new routines to make list and replacing
835      pressure by totPhiHyd).
836    o Updated and merged grdchk package
837      - has both ADM and TLM checks
838      - works for single- and multi-proc.
839      - output cleaned
840      - worked successfully for parallel DIVA
841    o genmake:
842      - Adding -platform=SP4
843      - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
844    o Modif. for DIVA:
845      ctrl_unpack should not be called in intermediate DIVA interval.
846      (similar thing would apply for active files such as
847      tbar, sbar, psbar, which should not be reinitialised;
848      only relevant for ecco-branch)
849    
850    checkpoint48h_post
851    o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
852    o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
853    o Added SEAICE_initialHEFF to pkg/seaice
854    o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
855    
856    checkpoint48g_post
857    --- EOS:
858    o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
859      store total Potential in totPhyHyd for diagnostics & EOS.
860    o fix restart and overlap Pb when using Z-coord and EOS funct. of P
861    --- Pressure/geopotential gradient:
862    o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
863    o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
864      ( changes results of global_ocean_pressure )
865    o NLFS + z-coord.: add eta*Rho' contribution.
866    o accurate phiHyd when using interface-W at the middle between 2 centers
867     ( changes results of ideal_2D_oce )
868    o includes r* 2nd term in potential gradient.
869    
870    checkpoint48f_post
871    Merging from release1_p12:
872    o Modifications for using pkg/exf with pkg/seaice
873      - improved description of the various forcing configurations
874      - added basic radiation bulk formulae to pkg/exf
875      - units/sign fix for evap computation in exf_getffields.F
876      - updated verification/global_with_exf/results/output.txt
877    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
878      (SBO) core products, including oceanic mass, center-of-mass,
879      angular, and bottom pressure (see pkg/sbo/README.sbo).
880    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
881      to avoid negative values in shallow regions.
882      - updated verification/natl_box/results/output.txt
883      - updated verification/lab_sea/results/output.txt
884    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
885    o Added useSingleCpuIO option (see PARAMS.h).
886    o Updated useSingleCpuIO option in mdsio_writefield.F to
887      work with multi-field files, e.g., for single-file pickup.
888    o pkg/seaice:
889      - bug fix in growth.F: QNET for no shortwave case
890      - added HeffFile for specifying initial sea-ice thickness
891      - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
892    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
893      kpp_transport_t.F, forward_step.F, and the_main_loop.F
894    o pkg/seaice:
895      - adjoint-friendly modifications
896      - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
897    
898    checkpoint48e_post
899    o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
900    o dynamics: change definition of computational domain & adapt mom_fluxform
901      accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
902    o following exp works with Olx=Oly=2 (and pass through checkbounds option):
903        adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
904        exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
905        global_ocean.90x40x15 global_with_exf global_ocean_pressure
906        inverted_barometer solid-body.cs-32x32x1
907      (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
908    
909    checkpoint48d_post
910    o in preparation for r*:
911     a) use pre-computed gradient of hydrostatic potential:
912        changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
913     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
914        => affects results of glob_oce_pressure (different truncation error)  
915      update output.txt of ideal_2D_oce & global_ocean_pressure
916    
917    checkpoint48d_pre
918    o in preparation for r*:
919      new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
920      pass the 2 comp. of the grad. as arguments to momentum S/R.
921      but for the moment, only used if it does not change the results.
922    o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
923    
924    checkpoint48c_post
925    Modifications in treatment of initial flux forcing controls
926    to avoid extra storing of flux fields.
927    
928    checkpoint48c_pre
929  o Added tidal_basin_2d experiment (currently 1D!)  o Added tidal_basin_2d experiment (currently 1D!)
930  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)
931    
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