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revision 1.127 by adcroft, Thu Jan 30 18:35:42 2003 UTC revision 1.333 by edhill, Wed Jul 21 16:34:46 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 genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
7    
8    checkpoint54c_post
9    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
10      this affects (truncation error) output.txt of test-exp:
11       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
12    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
13    o change Qnet to always be the net heat flux, (+upward).
14      affects (truncation error) output of natl_box exp.: updated
15    o define the max number of passive tracers in PTRACERS_SIZE.h
16    o start to test mnc routinely in exp0
17    o add sea-ice loading (sIceLoad) as a new forcing field.
18    
19    checkpoint54b_post
20    o add testreport "-j JOBS" option for parallel builds (tested and pretty
21       impressive on Altix and Opteron systems)
22    o diagnostics can now write NetCDF files through the mnc package
23    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
24    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
25    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
26      affects (truncation error) output of lab_sea & natl_box exp.: updated
27    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
28    
29    checkpoint54a_post
30    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
31    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
32    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
33    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
34      + internal_wave (shift in writing cg2d_ini_res)
35    checkpoint54a_pre
36    
37    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
38      - modified verification/lab_sea and natl_box_adjoint accordingly
39    
40    checkpoint54
41    checkpoint53g_post
42    o prepare splitting of thermodynamics: store convect.counter in common block
43    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
44      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
45    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
46    o new parameter "nShapS": allow to treat differently S from T (nShapT)
47    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
48    o restore adjointability
49    
50    checkpoint53f_post
51    o modifications that affect AIM experiment results (update output.txt):
52      - no advection of S at top interface Nr (pkg/generic_advdiff)
53      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
54    o AIM pkg:
55      - include stability function into surf.Flux derivative relative to Tsurf
56      - calculate clear-sky radiation & surface temp. change (for diagnostics)
57    
58    checkpoint53e_post
59    o merged cylindrical coord configuration
60    o added rotating_tank experiment
61    checkpoint53e_pre
62    
63    checkpoint53d_post
64    o faulks upgraded: re-generate output.txt that have changed:
65       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
66    o Added Bryan and Lewis, 1979, vertical diffusivity profile
67    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
68    o added Sadourny discretization of Coriolis
69      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
70      - re-enabled use of omega3 (useAbsVorticity)
71    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
72      vector-invariant equations
73      - note: does *NOT* yet use same variable visc. for no-slip BC's.
74    o recoded the lateral boundary conditions for non-hydrostatic w, this time
75      hopefully without new bugs
76      - still to do: biharmonic friction for non-hydrostatic w
77    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
78    o regenerated output for global_ocean_ebm (using -ieee)
79    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
80      of mom_common/
81      - simple re-arrangement of instructions within computing loop
82    checkpoint53d_pre
83    
84    checkpoint53c_post
85    o new version of coupler for AIM+thSIce and Ocean models
86     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
87     - land: change Evaporation of snow
88     - aim with thSIce: fix bug in snow-precip.
89    o changes to calc_gw.F
90     - bug fix for w^2 term near the bottom boundary
91     - (hopefully) improve the lateral slip boundary condtions for use with
92        partial/looped cells
93      - because the bug fix changes two verification experiments anyway (exp5
94        and plume on slope), change the lateral boundary condition from half slip
95        to the value of no_slip_sides
96    o ebm package wasnt quite up to the parallel task. Fixed that.
97    o Adjoint of EBM package + verification
98      * TLM OK
99      * ADM not sufficient accuracy yet (needs further testing)
100    
101    checkpoint53b_post
102    o Commiting new energy balance model to repository
103      * package is pkg/ebm
104      * verif. is verification/global_ocean_ebm
105      * references are in ebm_driver.F
106    C      * X. Wang, P. Stone and J. Marotzke, 1999:
107    C        Global thermohaline circulation. Part I:
108    C        Sensitivity to atmospheric moisture transport.
109    C        J. Climate 12(1), 71-82
110    C      * X. Wang, P. Stone and J. Marotzke, 1999:
111    C        Global thermohaline circulation. Part II:
112    C        Sensitivity with interactive transport.
113    C        J. Climate 12(1), 83-91
114    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
115    C        Destabilization of the thermohaline circulation
116    C        by atmospheric eddy transports.
117    C        J. Climate 7(12), 1870-1882
118    o Will need long integration testing.
119    checkpoint53b_pre
120    
121    o created pkg/mom_common in preparation for variable viscosity code
122    o renamed and split ini_mnc_io
123    o pkg/land: only liquid water can diffuse or run-off
124    o AIM using land: soil wetness availability account for snow
125    o added printMapIncludesZeros to EEPARMS namelist
126    
127    checkpoint53a_post
128    o restore TAMC compatiility for exf_constants.h
129      (no usage of _d in .h)
130    o Additional storing in KPP in an attempt to fix
131      TAMC problem with adjoint of KPP code.
132      (no success...)
133      Identical code works fine with TAF.
134    o Fixed verification/natl_box_adjoint experiments.
135      Initial conditions for Experiments 4 and 5 are now
136      set to "SEAICE_initialHEFF=0", which is more reasonable,
137      and hence gives results closer to that of Experiment 2.
138      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
139    
140    checkpoint53
141    o stable checkpoint with up to date adjoint
142      TLM tests only run for 1st grdchk at the moment. Its unclear if
143      this is a code problem or a problem with resetting code for g_
144      variables that is being autogenerated wrong.
145      Otherwise:
146       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
147       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
148         are both still in chaos following their security messes.
149    
150    checkpoint52n_post
151    o various build (mostly genmake2) changes including:
152      - ability to build/run more easily within Cygwin and MacOS X
153      - more complicated Makefiles with a stronger dependence on Gnu Make
154    o pkg/seaice modifications
155      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
156        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
157        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
158      - changed proxy for geostrophic velocity and updated
159        verification/lab_sea/results/* accordingly
160      - removed ADI dynamic solver from pkg/seaice
161      - replaced all occurrences of 1/CSTICE or 1/CSUICE
162        they caused a segmentation fault under certain circumstances
163      - removed unused field WATR
164    o bug fix in exf-package:
165      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
166         now reflect that.
167    o small fixes in the cal-package:
168      - set reference date to first of January for the 'model'-calendar
169      - failing of cal_CheckDate in cal_FullDate now actually results in a
170        warning
171    o small modifications in exf-package to increase flexibility:
172      - change climtempfreeze from a constant to a runtime parameter that
173        is specified in data.exf_clim (default = -1.9)
174      - introduce runtime parameter windstressmax (default = 2.0) that is
175        specified in data.exf
176    o fix in pkg/thsice:
177      - update Evap (Tsf changes) to be consistent with Latent heat flux
178      - maintain snow precipitation unchanged (even if Tsf >=0).
179     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
180    
181    checkpoint52m_post
182    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
183      this does not change any of the results, because myIter=0 in swfrac always
184      lead to jwtype=2 (the default anyway), but the call makes little sense
185      as a default
186    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
187    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
188      atmospheric model (AIM) to use it ; add a "slab ocean" component.
189    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
190    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
191    o extending useSingleCpuIO option to work with new exch2 I/O format
192      - old-style, missing-tile I/O is still accessible by defining CPP
193        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
194    o monitor package can write to NetCDF files and/or STDOUT
195    o fix re-definition bug in MNC_GRID_INIT_ALL()
196    o doc/api_reference added
197      - a framework for building an API Reference Manual using all
198        the "protex" comments embedded in the code
199      - see pkg/generic_advdiff, pkg/mnc for examples
200    o MNC:
201      - make myThid the last argument for all subroutines
202      - new default for the grid files: NO halos
203      - add useMNC and other run-time flags
204      - separate per-file-group handling of the unlimited dimension
205      - early initialization of MNC w/ flags read at the eeboot stage
206        and lookup tables set in initialize_fixed
207      - write all MNC output to a freshly-created directory
208    o thermodynamics sea-ice (thsice) is now tested with testreport.
209    o test exp. advect_cs: use the standard cs32 grid ; update output.
210    o Added functionality to grdchk:
211      pick global i,j,k position (or nearest wet) where to perform check.
212    
213    checkpoint52l_post
214    o new land formulation:
215      a) use ground enthalpy as prognostic variable to ensure exact
216         energy conservation.
217      b) account for water temperature and for latent heat of freezing
218         in all processes (rain, run-off, ground storage)
219      c) compute surface and ground temperature implicitly.
220    o aim_v23 modification for new land model:
221      a) Treat separately land / ocean / sea-ice surface fluxes
222         to allow implicit computation of land & sea-ice surface temp.
223      b) add snow precipitation.
224    checkpoint52l_pre
225    
226    o fix problem (when 1 tile is empty) in min/max monitor.
227    o fix bug in timeAve (u,vZetatave in common block)
228    o no restoring terms under ice for pkg/seaice
229    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
230    o bug fix for pkg/seaice pickups
231    o change MNC call locations and add coordinate attributes
232    o mask vorticity at the corner ; affects global_ocean.cs output
233    o fix ini_curvilinear_grid ; test CS experiments with mpi
234    o aim.5l_cs: modify sea-ice fraction input file ; update output
235    o exf: Adding simple range check routine for exf fields after read
236    
237    checkpoint52k_post
238    o removed top-level directory "diags"
239      - we migrated these functions to pkg/timeave a long time ago
240    o fixed bug introduced in pkg/monitor
241    o accuracy ctrlprec = 32 insuffient for gradient checks using
242      averaged fields (I/O via cost_averages)
243      -> use ctrl.h in active_file*.F to control I/O precision.
244    o paramter list of CALL ADTHE_MAIN_LOOP
245    o added initial do_the_model_io to ecco
246    o set all ...Freq to zero after cost_final
247      taveFreq, dumpFreq, pChkptFreq
248    o MAIN and ECCO differentiability restored
249    
250    checkpoint52j_post
251    o fix nchklev in tamc.h for global_ocean...
252    o Bringing flow and store directives up-to-date
253    o Really weird thing!
254      call do_the_model_io from the_main_loop with parameters
255      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
256      TAF places a faulty re-call of initialise_varia
257      after cost_final call which should not be there!
258    checkpoint52j_pre
259    
260    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
261      error messages
262    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
263    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
264      debug output
265    o modfied mdsio_writefield.F to handle non-global files under exch2
266    o update AIM Cubed-Sphere exp (aim.5l_cs):
267      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
268    o update AIM Equatorial Channel exp:
269      use standard aim_v23 pkg and change the SST fields to be more realistic.
270    o globalFile now works with exch2
271    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
272      mon_vort3.F to make exch2 friendly with >1 tile per cube face
273    o limit timeave output for hi-res integrations
274    
275    checkpoint52i_post
276    o removed CPP_EEOPTIONS.h from verification/*/code
277    o updated the tiling for global_ocean_pressure
278    checkpoint52i_pre
279    
280    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
281      the old pkg/aim).
282    
283    checkpoint52h_pre
284    o shortened offending lines in exch2_send_rx?.template
285    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
286    o genmake2: add build & execute test for NetCDF code
287    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
288      old grid files, moved CPP_EEMACROS.h to pkg/exch2
289    o added useSingleCPUIO flag to monitor.F and mon_out.F
290    o added temporary hack for sea-ice dynamics on the cube:
291      metric terms are ignored and it is assumed that
292      there is no sea-ice on cube faces 1, 2, 4, and 5.
293    
294    checkpoint52f_post
295    o added exch2 cube routines to pkg/exch2
296    o modified hs94.cs-32x32x5 to use it
297    o added new grid files to hs94.cs-32x32x5
298    checkpoint52f_pre
299    
300    checkpoint52e_post
301    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
302      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
303    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
304      to work with implicit vertical advection and AB ;
305    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
306    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
307     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
308    checkpoint52e_pre
309    
310    o fix bug in impldiff when Nr=1 or Nr=2.
311    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
312    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
313    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
314      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
315    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
316    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
317    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
318    
319    checkpoint52d_post
320    o re-tiled many expts to allow comparison in multi-processor mode
321      - updated output accordingly
322      - changed hs94.128x64x5 to use intial T from file rather than use the
323        random number generator
324    o add infrastructure in model routines for fizhi and gridalt packages
325    o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
326    o changes to permit hi-res, cubed-sphere, configuration
327      - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
328      - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
329      - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
330        of surface winds for the cube
331      (A verification experiment, based on global_ocean.cs32x15, but with
332       pkg/seaice turned on and with on-the-fly interpolation from the NCEP
333       Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
334       complete with example surface forcing files and matlab scripts to look
335       at the output and compare it with that of global_ocean.cs32x15.)
336    o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
337       but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
338       to conform to the common rule.
339    o check-in the first version of the coupler + interfaces for multi-components
340       set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
341       - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
342       - atmosphere: use pkg aim_v23 ; no sea-ice for now.
343       - ocean and atmos. share the same horizontal grid (no interpolation).
344       - exchanges between component and coupler is done in forward_step
345    o new verification experiment, cpl_aim+ocn:
346       coupled ocean - AIM atmosphere on cs32 grid.
347    
348    checkpoint52d_pre
349    o surface flux time-av diagnostic modified for NLFS & RealFreshWater
350    o add call to AIM pendant S/R in external_forcing & external_fields_load.F
351    
352    checkpoint52c_post
353    o Fixing OPTIONS files for use of exf:
354      - ALLOW_ECCO not needed
355      - ECCO_CPPOPTIONS.h should not be included from
356        EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
357        as has been the case in the past
358      - All cal/exf related options are currently set in
359        single header file. Should remain so until we
360        agree on a consistent new policy.
361    o Removed all CPP options for cal package.
362      cal has no more CPP options.
363    o modified STOREs in GAD_ADVECTION
364    o corrected key comp. for passkey
365    
366    checkpoint52b_post
367    o new version: "thsice" of thermodynamic sea-ice pkg:
368     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
369     - modify fluxes but do not change theta directly;
370     - light cleaning of bulk_force pkg (still needed with thsice).
371     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
372       + output_thsice.txt to test thsice & bulk_force pkgs.
373    o put back grid & coriolis monitor output.
374    checkpoint52b_pre
375    
376    o call "do_the_model_io" at the beginning (=> dump initial state)
377    o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
378    o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
379      (need info on NUMBER_OF_PTRACERS)
380    o missing PTRACERS headers in some routines
381    o default tamc.h in pkg/autodiff supposed to crash
382      to ensure proper customization
383    
384    checkpoint52a_post
385    o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
386      - moved surfaceTendencyTice from pkg/seaice to main code
387      - subroutine FREEZE_SURFACE now limits only surface temperature
388        and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
389        => new output.txt for global_ocean.cs32x15 & global_with_exf
390      - keep the old version of FREEZE for backward compatibility;
391        global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
392      - corresponding modifs for TAF directives
393    o added surface flux output variables to TIMEAVE_STATVARS
394    o time-averaged output for pkg/ptracers
395    o fix problem with ECCO-related divided adjoint
396      snapshot file was missing some ad-variables,
397      but no warning issued by TAF
398    
399    checkpoint52a_pre
400    o some bug fixes for #undef REAL4_IS_SLOW
401    
402    checkpoint52 = ecco_c52_e35
403    o after testing adjoints of checkpoint51u_post
404    
405    checkpoint51u_post
406    o this is the post-merge tag of the ecco-branch
407      (needs another clean checkout and re-testing)
408    o various natl_box_adjoint configs and results
409      but no input fields
410    o obcs adjoint not yet merged!
411    o adding ECCO global 1x1 and 2x2 degree configs
412    o updated/extended some store directives for seaice
413    o pkg/ecco now containes ecco-specific part of cost function
414    o top level routines the_main_loop, forward_step
415      supersede those in model/src/
416      previous input data.cost now in data.ecco
417      (new namelist ecco_cost_nml)
418    o in ctrl/ cleaned some cross-dependencies and updated CPP options
419    
420    checkpoint51t_post
421    o this is the pre-merge tag of the ecco-branch
422    
423    checkpoint51s_post
424    o cleanup: removed various obsolete #define-s
425    o pkg/grdchk
426      - renamed 'ph-grd 3' to 'grad-res'
427      - merged from ecco-branch
428        (remaining bug fixes for obcs gradient checks)
429      - additional high-precision output for testreport
430        (grep for 'precision_grdchk_result')
431    
432    checkpoint51r_post
433    o cleaned up or removed CPP_OPTIONS.h files
434    o updated results for some of the tests to reflect the new
435      optfiles (-ieee: -O0 instead of -O3)
436    
437    checkpoint51q_post
438    o cd_code:
439      - moved cd_scheme.F -> cd_code_scheme.F
440      - separate read_checkpoint from cd_code_ini_vars.F
441      - separated cd_code part from write_checkpoint
442      - updated AD_SOURCE, generated .flow
443      - added CD_CODE_VARS.h to the_main_loop
444      - Moving cd_code specific store dir.s to pkg/cd_code
445    o ctrl package totally restructured
446      - pack/unpack now optional and decoupled from
447        xx_/adxx_ I/O
448      - ctrl_pack/unpack cleaned
449        (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
450      - confined inclusion of AD_CONFIG.h to where necessary.
451    o genmake2: changed AD dependencies from SRCFILES to AD_FILES
452    
453    checkpoint51p_post
454    o create initial cd_code package
455      - WARNING: the initialization of fields within packages
456        is broken because INI_FIELDS (where READ_CHECKPOINT is
457        called) is called *before* PACKAGES_INIT_VARIABLES.
458        This seems to be backwards since
459        1) its important to initially zero the entire field including
460           the "halo" region
461        2) zeroing needs to be done *before* reading pickup info
462           and the pickup call might or might not happen in any
463           particular run
464      - this needs an overhaul for R2
465    o cleanup verification/*/code/GMREDI_OPTIONS.h
466    o cleanup testreport
467    
468    checkpoint51o_post
469    o bringing AD-related verif's up to date with genmake2
470      - carbon/
471      - global_ocean.90x40x15/
472      - hs.94.1x64x5/
473      - (front_relax/ )
474    o (more) consistent directory structure for AD-related verif.'s
475    o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
476    o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
477    o bug fix in find_alpha.F for MDJWF:
478      - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
479        change rho -> rho-rhoConst
480      - replace call find_rho to find_rhonum
481    o initialisation of rFlx extended to full array (required by TAF)
482      and shifted to thermodynamics
483    o removed PTRACERS.h in ptracers routine
484    o added surfacetendencyPtr to S/R parameter list pracers_forcing
485    o Correcting initialisations for fVerU, fVerV.
486    o helping TAF to recognize dependency on kUp for
487      fVerU, fVerV
488    o Replacing delZ by delR in pkg/ctrl/
489    checkpoint51o_pre
490    
491    o undid all of cp51 pending some cleanups and discussion
492    o added the [#include "AD_CONFIG.h"] statement to all files that need
493       it for adjoint/tl #defines
494     o re-worked the build logic in genmake2 to support AD_CONFIG.h
495     o removed tools/genmake since it no longer works
496    
497    checkpoint51n_post
498    o modifications to make FREEZE flux visible to pkg/kpp
499      - moved surfaceTendencyTice from pkg/seaice to main code
500      - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
501      - subroutine FREEZE now limits only surface temperature
502        (this means new output.txt for global_ocean.90x40x15,
503         global_ocean.cs32x15, and global_with_exf)
504    o added surface flux output variables to TIMEAVE_STATVARS
505    
506    checkpoint51n_pre
507    o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
508    o added [#include "AD_CONFIG.h"] to all files that use the following
509      defines:
510      - ALLOW_ADJOINT_RUN
511      - ALLOW_TANGENTLINEAR_RUN
512      - ALLOW_ECCO_OPTIMIZATION
513    
514    checkpoint51m_post
515    o incorporating changes to get TAMC/TAF working in genmake2
516      - added new TAMC/TAF targets to the Makefile
517      - various cleanups related to package handling
518      - these changes should have no impact on the forward model
519    
520    checkpoint51l_post
521    o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
522     - faster algorithm for cal_addtime.F
523     - higher precision arithmetic, where needed
524     - pkg/exf *startdate variables changed from calendar date to
525       model integration time
526    
527    checkpoint51l_pre
528    o add salt flux to forcing fields (used when salty sea-ice forms or melts)
529    o enable to apply restoring on S & T only in a latitude band.
530    o update output (external_forcing_surf modif. change truncation errors)
531       global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
532    
533    checkpoint51k_post
534    o change default to: useNHMTerms=.FALSE.
535     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
536       adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
537     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
538        exp1, ideal_2D_oce
539     - change data file of oceanic exp (leave the results unchanged for now)
540       exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
541    o set gravitySign automatically according to the vertical coordinate used
542      (and change sign: back to "logical" value: +1 when R increases downward)
543    o added an include barrier to the default CPP_OPTIONS.h and
544      removed the #include "PACKAGES_CONFIG.h" from it
545    o fix a bug in mom_fluxform (from chk51j_post)
546    
547    checkpoint51j_post
548    o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
549    o adjusted some flow directives (dynamics, thermodynamics)
550    o added cubed-sphere case to test cost function
551    o heckpoint_lev?_directives.h now include
552      pkg-specific directives, whenever those are enabled.
553    o Moving pkg-specific flow directives to corresponding pkg
554      Moving pkg-specific differentiation list to corresponding pkg
555      Moving pkg-specific checkpoint-lev storing to corresponding pkg
556      ---> conventions are
557           - pkg_ad.flow
558           - pkg_ad_diff.list
559           - pkg_ad_check_lev?_dir.h
560    
561    checkpoint51i_post
562    o merge of the branch-genmake2
563      - knowingly breaks the older genmake
564      - automatic generation of all ALLOW_${PKG_NAME} defines
565      - new testreport supersedes older testscript
566    o large number of package inclusion and header cleanups
567    checkpoint51i_pre
568    
569    o new output for adjoin of global ocean vector invariant
570    o fix for checkpoint of thermodynamic seaice and bulk_force
571    o Steph gchem various cleanups
572    
573    checkpoint 51h_pre
574    o fixed some single quotes
575    o modify gchem pkg to be more versatile
576    o modifications to clean up dic pkg
577    o add pkg/cfc
578    
579    checkpoint51g_post
580    o provide links for ARPACK and ADM*TLM
581    o start removing verification/vero/
582    o update AD-related stuff
583      (in particular some IF-statements in model/src/ routines)
584    o adding to verification/global_ocean.90x40x15/ adjoint of
585      vector invariant setup
586    
587    checkpoint51f_post
588    o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
589    o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
590      of tracer Green's fucntions for ocean inversion project.
591    
592    checkpoint51f_pre
593    o Added on-the-fly spatial interpolation capability
594        "USE_EXF_INTERPOLATION" to pkg/exf.
595      - This is a temporary Cartesian-grid hack until
596        the super-duper ESMF coupler becomes available.
597      - See verification/global_with_exf/README for usage example.
598      - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
599        flags and modified pkg/seaice accordingly.
600    o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
601        and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
602        non-local transport term.
603    
604    checkpoint51e_post
605    o pkg/mom_vecinv:
606      - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
607      - add time-ave diagnostic of vorticity advection.
608    o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
609    o atmospheric geopotential: - include water vapor effect;
610                                - use p^kappa in p* scaling.
611    o land pkg: read initial state from files.
612    o AIM : add stratospheric drag in the upper level
613    
614    checkpoint51d_post
615    o change function ILNBLNK (=> last non-blank char.) to return zero
616      (instead of the string length) when the string. char is empty
617    o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
618    o modif's to restore TAMC compatibility
619      - avoid "_d" constructs in PARAMETER declarations
620      - avoid interrupting lines by comment lines
621    o Use cluster local disks for purely local I/O
622      vs. globally visible disks needed for ctrl stuff
623      (merged from ecco-branch)
624      - new active_file_loc... and mdsio_..._loc routines
625      - affected packages: autodiff, ctrl, grdchk, mdsio
626    
627    checkpoint51c_post
628    o introducing integer flag debugLevel
629      - debLevZero: suppress all output
630      - debLevA: standard
631      - debLevB: equivalent to current debugMode=.TRUE.
632    o introducing pathname variable mdsioLocalDir for mdsio
633      that can be specified at runtime
634      (relevant for cluster I/O to local disk)
635    `
636    >>>checkpoint51b_post
637    adjoint of ptracers
638    o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
639    o extended state in checkpoint_lev?, etc.
640    o alternative ctrl/cost with tr1 or ptracer
641    o new comlev1_bibj_ptracers
642    o new ptracers.flow
643    o made ptracers_forcing same as external_forcing_s
644    o added verification for adjoint with ptracers
645      - adm. grdchk fail so far
646      - tlm. grdchk OK
647      - checked tapelev/comlev recomputations: OK
648    <<<checkpoint51b_pre
649    
650    checkpoint51a_post
651    o added code for biogeochemistry package
652      - new pkgs: dic, gchem
653      - new subroutine in ptracers
654    o modify code for biogeo packages
655      - in model/src and pkg/ptracers
656    
657    checkpoint51
658    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
659      - autodiff, ctrl, exf, grdchk, seaice
660      kept separate packages
661      - cost, ecco, obcs
662    o updating verification/internal_wave, verification/lab_sea
663      (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
664    
665    checkpoint50i_post
666    o Preparing next differentiable checkpoint and sync
667      of MAIN vs. ecco-branch
668      - 1st step: this one is differentiable
669      - 2nd step: next(! not this) checkpoint will have updated packages
670                  from ecco-branch)
671    
672    checkpoint50h_post
673    o new package "land": provide surface BC for AIM.
674    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
675    o AIM: use true log-P extrapolation for near surface temp (= as in
676        F.Molteni paper) ; update aim.5l_cs output.
677    o New variable in PARM03 for more flexible pickups
678    o somewhat cleaned package initialisation sequence for
679      ctrl/ cost/ ecco/ in packages_... routines
680    
681    checkpoint50g_post
682    o merged with release1_p17 (pkg/seaice and verification/lab_sea)
683      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
684      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
685        made the default because of faster convergence than ADI
686    
687    checkpoint50f_post
688    o exf totally restructured
689      - replaced all exf_set_ routines by one generic exf_set_gen.F
690        and made sure it's still differentiable
691      - split exf_getffields.F into new exf_bulkformulae.F
692      - exf_inscal_/exf_outscal_ suffixes consistent with field names
693      - updated adjoint/makefile and relevant verif. accordingly
694    
695    checkpoint50f_pre
696     o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
697          + change Evap over land. (update aim.5l_cs output)
698     o added missing .cvsignores and made uniform across expts
699     o changed configuration of tidal_basin_2d expt
700     o added pkg/debug functions for tracing code in fatal crashes
701     o tidied pkg/monitor to use MONITOR_OPTIONS.h
702     o new fn in pkg/monitor to stop model if solution grows too big
703     o removed lots of single quotes from comments
704    
705    checkpoint50e_post
706    o make KPP work with PTRACERS
707     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
708       nearly a copy of kpp_transport_s
709     - there is no analogue to SurfaceTendencyS, so I have to use
710       gPtr(of the surface layer) instead
711    o add a new platform SunFire+mpi (SunFire 15000) to genmake
712    checkpoint50e_pre
713    
714    checkpoint50d_post
715    o change kpp output from multiple-record state files to single-record state
716      files analogous to write_state.F
717    o reduce the output frequency of cg3d-related stuff to the monitor frequency,
718      analogous to the cg2d-related output.
719    o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
720      so that writing to internal file fn (with length 512) fails.
721    checkpoint50d_pre
722    
723    checkpoint50c_post
724    o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
725    o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
726    o add time-average diagnostic of U*V and vertical diffusive flux for theta.
727    o bug fixed in convective adjustment diagnostic (multi-tile set-up).
728    o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
729    
730    checkpoint50c_pre
731    Merging from release1_p13:
732    o bug fix for pkg/seaice dynamic solver
733    o Added SEAICE_initialHEFF to pkg/seaice
734    
735    checkpoint50b_post
736    o store u*,v* in gU,V instead of in guNm1,gvNm1
737    o in order to put the momForcing out of the Adams-Bashforth:
738      move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
739      to timestep.F
740    o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
741    o re-generate output for highly sensitive test-exp:
742       global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
743    
744    checkpoint50b_pre
745    o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
746    o corrected CPP option mismatch in exf_Bulk... functions for case
747      #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
748    
749    checkpoint50a_post
750    o Bug fix for merging between c50 and KPP.
751      ikey was passed from thermodynamics to kpp_calc via
752      common block rather than being recomputed in kpp_calc,
753      in contradiction with new key itdkey.
754      New key ikppkey created, and tamc.h headers updated.
755    
756    checkpoint50
757    - 2nd step of merge with ecco-branch:
758      merge changes in ecco-branch back into main trunk
759    - bug fix in find_alpha
760    - more storing in gmredi_calc_tensor.F, kpp_routines.F
761    - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
762    - merged some sliced AD support routines
763    
764    checkpoint49
765    merged from ecco-branch:
766    o exf:
767      - Enable initialisation of forcing fields to constant
768        (runtime) values.
769      - in exf_getffields.F
770        Reduce i-/j-loop to interior domain, discarding overlaps.
771        That also fixes wrong TAF-key computations for key_1, key_2
772        with bulf formulae.
773      - exf_init.F modify #ifdef for exf_init_evap
774      - exf_getffieldrec.F, ctrl_getrec.F
775        The following INT-usages are not safe:
776          fldsecs  = int(fldsecs/fldperiod)*fldperiod
777          fldcount = int(fldsecs/fldperiod) + 1
778        and were modified.
779    o autodiff: checkpoint_lev...
780      - updated storing for bulk formulae (some arrays were missing)
781      - added state for seaice package
782      - synchronized with main branch
783    o DIVA:
784      Modif.s in
785      - the_main_loop.F
786      - the_model_main.F
787      and added cost_final_restore.F cost_final_store.F
788      o With these changes, it is possible to fully separate
789        the first forward run to compute the cost function (mdthe_main_loop)
790        and adjoint runs over individual DIVA intervals (adthe_main_loop)
791        into separate model executions.
792        This enables better tuning of DIVA to given queue sizes.
793      o Loss of cost function value in consecutive DIVA runs is
794        fixed by storing to 'costfinal' file.
795      o Appropriate call of ctrl_unpack/_pack,grdchk_main at
796        beginning/end of adjoint integration is accounted for.
797      The current changes apply to TAF-1.4.26.
798      TAF has one remaining bug, requiring one manual change
799      (see MITgcm manual).
800    o cal: synchronized between MAIN and ecco-branch
801    
802    checkpoint48i_post
803    o Changes to restore differentiability of code w.r.t. previous tag
804      (mostly adding new routines to make list and replacing
805      pressure by totPhiHyd).
806    o Updated and merged grdchk package
807      - has both ADM and TLM checks
808      - works for single- and multi-proc.
809      - output cleaned
810      - worked successfully for parallel DIVA
811    o genmake:
812      - Adding -platform=SP4
813      - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
814    o Modif. for DIVA:
815      ctrl_unpack should not be called in intermediate DIVA interval.
816      (similar thing would apply for active files such as
817      tbar, sbar, psbar, which should not be reinitialised;
818      only relevant for ecco-branch)
819    
820    checkpoint48h_post
821    o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
822    o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
823    o Added SEAICE_initialHEFF to pkg/seaice
824    o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
825    
826    checkpoint48g_post
827    --- EOS:
828    o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
829      store total Potential in totPhyHyd for diagnostics & EOS.
830    o fix restart and overlap Pb when using Z-coord and EOS funct. of P
831    --- Pressure/geopotential gradient:
832    o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
833    o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
834      ( changes results of global_ocean_pressure )
835    o NLFS + z-coord.: add eta*Rho' contribution.
836    o accurate phiHyd when using interface-W at the middle between 2 centers
837     ( changes results of ideal_2D_oce )
838    o includes r* 2nd term in potential gradient.
839    
840    checkpoint48f_post
841    Merging from release1_p12:
842    o Modifications for using pkg/exf with pkg/seaice
843      - improved description of the various forcing configurations
844      - added basic radiation bulk formulae to pkg/exf
845      - units/sign fix for evap computation in exf_getffields.F
846      - updated verification/global_with_exf/results/output.txt
847    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
848      (SBO) core products, including oceanic mass, center-of-mass,
849      angular, and bottom pressure (see pkg/sbo/README.sbo).
850    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
851      to avoid negative values in shallow regions.
852      - updated verification/natl_box/results/output.txt
853      - updated verification/lab_sea/results/output.txt
854    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
855    o Added useSingleCpuIO option (see PARAMS.h).
856    o Updated useSingleCpuIO option in mdsio_writefield.F to
857      work with multi-field files, e.g., for single-file pickup.
858    o pkg/seaice:
859      - bug fix in growth.F: QNET for no shortwave case
860      - added HeffFile for specifying initial sea-ice thickness
861      - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
862    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
863      kpp_transport_t.F, forward_step.F, and the_main_loop.F
864    o pkg/seaice:
865      - adjoint-friendly modifications
866      - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
867    
868    checkpoint48e_post
869    o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
870    o dynamics: change definition of computational domain & adapt mom_fluxform
871      accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
872    o following exp works with Olx=Oly=2 (and pass through checkbounds option):
873        adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
874        exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
875        global_ocean.90x40x15 global_with_exf global_ocean_pressure
876        inverted_barometer solid-body.cs-32x32x1
877      (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
878    
879    checkpoint48d_post
880    o in preparation for r*:
881     a) use pre-computed gradient of hydrostatic potential:
882        changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
883     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
884        => affects results of glob_oce_pressure (different truncation error)  
885      update output.txt of ideal_2D_oce & global_ocean_pressure
886    
887    checkpoint48d_pre
888    o in preparation for r*:
889      new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
890      pass the 2 comp. of the grad. as arguments to momentum S/R.
891      but for the moment, only used if it does not change the results.
892    o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
893    
894    checkpoint48c_post
895    Modifications in treatment of initial flux forcing controls
896    to avoid extra storing of flux fields.
897    
898    checkpoint48c_pre
899  o Added tidal_basin_2d experiment (currently 1D!)  o Added tidal_basin_2d experiment (currently 1D!)
900  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)
901    
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