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revision 1.127 by adcroft, Thu Jan 30 18:35:42 2003 UTC revision 1.344 by mlosch, Thu Sep 16 12:40:37 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 two new packages
7      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
8        + subject to optimization (memory)
9      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
10        + subject to reordering (many GOTOs in the original code)
11        + so far opps is called for every (i,j) point, and then operates in
12          the vertical; one may want to reorder the scheme in order operate in
13          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
14          fields)
15    o overhaul of IO so that we now have flags for MDSIO and/or MNC
16      - all verification tests compile and run with linux_ia32_g77
17      - defaults are compatible with current input files--nothing
18        should change if you were not previously using MNC
19      - MNC output has been added in numerous places (eg. timeave)
20        but there are still a few writes not yet do-able with MNC
21        (this is in progress)
22      - flags now allow for either/or/both use of MDSIO and MNC and
23        documentation will soon follow
24      - numerous small formatting cleanups for ProTeX
25    o add version info (via BUILD_INFO.h) to MNC and stdout
26    
27    checkpoint54e_post
28    o add two new packages
29      - pp81 (Packanowski and Philander, 1981), Richardson number and
30        stratification dependent mixing
31      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
32      - these scheme operate in a similar manner as KPP (without ghat, of
33        course), however there is only one diffusivity that is used for both
34        temperature and salinity (and passive tracers)ç
35    o add offline package
36    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
37      provided by Stephanie Dutkiewicz
38    o genmake2: add ability to search for C compilers and cleanup test output
39      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
40    
41    checkpoint54d_post
42    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
43    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
44      leading to additional shift by 5 days each year of integration
45       (i.e. leading to considerable offset over the years)
46    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
47    o start with no AB and no initial filtering (staggerTimeStep):
48      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
49    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
50      (external loading & cpl import/export stay in forward_step.F)
51    o update coupling interface to work with new staggerTimeStep
52    o change MDSIO ptracers_pickup.
53    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
54    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
55    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
56    
57    checkpoint54c_post
58    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
59      this affects (truncation error) output.txt of test-exp:
60       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
61    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
62    o change Qnet to always be the net heat flux, (+upward).
63      affects (truncation error) output of natl_box exp.: updated
64    o define the max number of passive tracers in PTRACERS_SIZE.h
65    o start to test mnc routinely in exp0
66    o add sea-ice loading (sIceLoad) as a new forcing field.
67    
68    checkpoint54b_post
69    o add testreport "-j JOBS" option for parallel builds (tested and pretty
70       impressive on Altix and Opteron systems)
71    o diagnostics can now write NetCDF files through the mnc package
72    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
73    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
74    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
75      affects (truncation error) output of lab_sea & natl_box exp.: updated
76    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
77    
78    checkpoint54a_post
79    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
80    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
81    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
82    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
83      + internal_wave (shift in writing cg2d_ini_res)
84    checkpoint54a_pre
85    
86    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
87      - modified verification/lab_sea and natl_box_adjoint accordingly
88    
89    checkpoint54
90    checkpoint53g_post
91    o prepare splitting of thermodynamics: store convect.counter in common block
92    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
93      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
94    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
95    o new parameter "nShapS": allow to treat differently S from T (nShapT)
96    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
97    o restore adjointability
98    
99    checkpoint53f_post
100    o modifications that affect AIM experiment results (update output.txt):
101      - no advection of S at top interface Nr (pkg/generic_advdiff)
102      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
103    o AIM pkg:
104      - include stability function into surf.Flux derivative relative to Tsurf
105      - calculate clear-sky radiation & surface temp. change (for diagnostics)
106    
107    checkpoint53e_post
108    o merged cylindrical coord configuration
109    o added rotating_tank experiment
110    checkpoint53e_pre
111    
112    checkpoint53d_post
113    o faulks upgraded: re-generate output.txt that have changed:
114       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
115    o Added Bryan and Lewis, 1979, vertical diffusivity profile
116    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
117    o added Sadourny discretization of Coriolis
118      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
119      - re-enabled use of omega3 (useAbsVorticity)
120    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
121      vector-invariant equations
122      - note: does *NOT* yet use same variable visc. for no-slip BC's.
123    o recoded the lateral boundary conditions for non-hydrostatic w, this time
124      hopefully without new bugs
125      - still to do: biharmonic friction for non-hydrostatic w
126    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
127    o regenerated output for global_ocean_ebm (using -ieee)
128    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
129      of mom_common/
130      - simple re-arrangement of instructions within computing loop
131    checkpoint53d_pre
132    
133    checkpoint53c_post
134    o new version of coupler for AIM+thSIce and Ocean models
135     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
136     - land: change Evaporation of snow
137     - aim with thSIce: fix bug in snow-precip.
138    o changes to calc_gw.F
139     - bug fix for w^2 term near the bottom boundary
140     - (hopefully) improve the lateral slip boundary condtions for use with
141        partial/looped cells
142      - because the bug fix changes two verification experiments anyway (exp5
143        and plume on slope), change the lateral boundary condition from half slip
144        to the value of no_slip_sides
145    o ebm package wasnt quite up to the parallel task. Fixed that.
146    o Adjoint of EBM package + verification
147      * TLM OK
148      * ADM not sufficient accuracy yet (needs further testing)
149    
150    checkpoint53b_post
151    o Commiting new energy balance model to repository
152      * package is pkg/ebm
153      * verif. is verification/global_ocean_ebm
154      * references are in ebm_driver.F
155    C      * X. Wang, P. Stone and J. Marotzke, 1999:
156    C        Global thermohaline circulation. Part I:
157    C        Sensitivity to atmospheric moisture transport.
158    C        J. Climate 12(1), 71-82
159    C      * X. Wang, P. Stone and J. Marotzke, 1999:
160    C        Global thermohaline circulation. Part II:
161    C        Sensitivity with interactive transport.
162    C        J. Climate 12(1), 83-91
163    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
164    C        Destabilization of the thermohaline circulation
165    C        by atmospheric eddy transports.
166    C        J. Climate 7(12), 1870-1882
167    o Will need long integration testing.
168    checkpoint53b_pre
169    
170    o created pkg/mom_common in preparation for variable viscosity code
171    o renamed and split ini_mnc_io
172    o pkg/land: only liquid water can diffuse or run-off
173    o AIM using land: soil wetness availability account for snow
174    o added printMapIncludesZeros to EEPARMS namelist
175    
176    checkpoint53a_post
177    o restore TAMC compatiility for exf_constants.h
178      (no usage of _d in .h)
179    o Additional storing in KPP in an attempt to fix
180      TAMC problem with adjoint of KPP code.
181      (no success...)
182      Identical code works fine with TAF.
183    o Fixed verification/natl_box_adjoint experiments.
184      Initial conditions for Experiments 4 and 5 are now
185      set to "SEAICE_initialHEFF=0", which is more reasonable,
186      and hence gives results closer to that of Experiment 2.
187      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
188    
189    checkpoint53
190    o stable checkpoint with up to date adjoint
191      TLM tests only run for 1st grdchk at the moment. Its unclear if
192      this is a code problem or a problem with resetting code for g_
193      variables that is being autogenerated wrong.
194      Otherwise:
195       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
196       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
197         are both still in chaos following their security messes.
198    
199    checkpoint52n_post
200    o various build (mostly genmake2) changes including:
201      - ability to build/run more easily within Cygwin and MacOS X
202      - more complicated Makefiles with a stronger dependence on Gnu Make
203    o pkg/seaice modifications
204      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
205        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
206        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
207      - changed proxy for geostrophic velocity and updated
208        verification/lab_sea/results/* accordingly
209      - removed ADI dynamic solver from pkg/seaice
210      - replaced all occurrences of 1/CSTICE or 1/CSUICE
211        they caused a segmentation fault under certain circumstances
212      - removed unused field WATR
213    o bug fix in exf-package:
214      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
215         now reflect that.
216    o small fixes in the cal-package:
217      - set reference date to first of January for the 'model'-calendar
218      - failing of cal_CheckDate in cal_FullDate now actually results in a
219        warning
220    o small modifications in exf-package to increase flexibility:
221      - change climtempfreeze from a constant to a runtime parameter that
222        is specified in data.exf_clim (default = -1.9)
223      - introduce runtime parameter windstressmax (default = 2.0) that is
224        specified in data.exf
225    o fix in pkg/thsice:
226      - update Evap (Tsf changes) to be consistent with Latent heat flux
227      - maintain snow precipitation unchanged (even if Tsf >=0).
228     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
229    
230    checkpoint52m_post
231    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
232      this does not change any of the results, because myIter=0 in swfrac always
233      lead to jwtype=2 (the default anyway), but the call makes little sense
234      as a default
235    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
236    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
237      atmospheric model (AIM) to use it ; add a "slab ocean" component.
238    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
239    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
240    o extending useSingleCpuIO option to work with new exch2 I/O format
241      - old-style, missing-tile I/O is still accessible by defining CPP
242        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
243    o monitor package can write to NetCDF files and/or STDOUT
244    o fix re-definition bug in MNC_GRID_INIT_ALL()
245    o doc/api_reference added
246      - a framework for building an API Reference Manual using all
247        the "protex" comments embedded in the code
248      - see pkg/generic_advdiff, pkg/mnc for examples
249    o MNC:
250      - make myThid the last argument for all subroutines
251      - new default for the grid files: NO halos
252      - add useMNC and other run-time flags
253      - separate per-file-group handling of the unlimited dimension
254      - early initialization of MNC w/ flags read at the eeboot stage
255        and lookup tables set in initialize_fixed
256      - write all MNC output to a freshly-created directory
257    o thermodynamics sea-ice (thsice) is now tested with testreport.
258    o test exp. advect_cs: use the standard cs32 grid ; update output.
259    o Added functionality to grdchk:
260      pick global i,j,k position (or nearest wet) where to perform check.
261    
262    checkpoint52l_post
263    o new land formulation:
264      a) use ground enthalpy as prognostic variable to ensure exact
265         energy conservation.
266      b) account for water temperature and for latent heat of freezing
267         in all processes (rain, run-off, ground storage)
268      c) compute surface and ground temperature implicitly.
269    o aim_v23 modification for new land model:
270      a) Treat separately land / ocean / sea-ice surface fluxes
271         to allow implicit computation of land & sea-ice surface temp.
272      b) add snow precipitation.
273    checkpoint52l_pre
274    
275    o fix problem (when 1 tile is empty) in min/max monitor.
276    o fix bug in timeAve (u,vZetatave in common block)
277    o no restoring terms under ice for pkg/seaice
278    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
279    o bug fix for pkg/seaice pickups
280    o change MNC call locations and add coordinate attributes
281    o mask vorticity at the corner ; affects global_ocean.cs output
282    o fix ini_curvilinear_grid ; test CS experiments with mpi
283    o aim.5l_cs: modify sea-ice fraction input file ; update output
284    o exf: Adding simple range check routine for exf fields after read
285    
286    checkpoint52k_post
287    o removed top-level directory "diags"
288      - we migrated these functions to pkg/timeave a long time ago
289    o fixed bug introduced in pkg/monitor
290    o accuracy ctrlprec = 32 insuffient for gradient checks using
291      averaged fields (I/O via cost_averages)
292      -> use ctrl.h in active_file*.F to control I/O precision.
293    o paramter list of CALL ADTHE_MAIN_LOOP
294    o added initial do_the_model_io to ecco
295    o set all ...Freq to zero after cost_final
296      taveFreq, dumpFreq, pChkptFreq
297    o MAIN and ECCO differentiability restored
298    
299    checkpoint52j_post
300    o fix nchklev in tamc.h for global_ocean...
301    o Bringing flow and store directives up-to-date
302    o Really weird thing!
303      call do_the_model_io from the_main_loop with parameters
304      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
305      TAF places a faulty re-call of initialise_varia
306      after cost_final call which should not be there!
307    checkpoint52j_pre
308    
309    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
310      error messages
311    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
312    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
313      debug output
314    o modfied mdsio_writefield.F to handle non-global files under exch2
315    o update AIM Cubed-Sphere exp (aim.5l_cs):
316      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
317    o update AIM Equatorial Channel exp:
318      use standard aim_v23 pkg and change the SST fields to be more realistic.
319    o globalFile now works with exch2
320    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
321      mon_vort3.F to make exch2 friendly with >1 tile per cube face
322    o limit timeave output for hi-res integrations
323    
324    checkpoint52i_post
325    o removed CPP_EEOPTIONS.h from verification/*/code
326    o updated the tiling for global_ocean_pressure
327    checkpoint52i_pre
328    
329    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
330      the old pkg/aim).
331    
332    checkpoint52h_pre
333    o shortened offending lines in exch2_send_rx?.template
334    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
335    o genmake2: add build & execute test for NetCDF code
336    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
337      old grid files, moved CPP_EEMACROS.h to pkg/exch2
338    o added useSingleCPUIO flag to monitor.F and mon_out.F
339    o added temporary hack for sea-ice dynamics on the cube:
340      metric terms are ignored and it is assumed that
341      there is no sea-ice on cube faces 1, 2, 4, and 5.
342    
343    checkpoint52f_post
344    o added exch2 cube routines to pkg/exch2
345    o modified hs94.cs-32x32x5 to use it
346    o added new grid files to hs94.cs-32x32x5
347    checkpoint52f_pre
348    
349    checkpoint52e_post
350    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
351      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
352    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
353      to work with implicit vertical advection and AB ;
354    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
355    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
356     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
357    checkpoint52e_pre
358    
359    o fix bug in impldiff when Nr=1 or Nr=2.
360    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
361    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
362    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
363      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
364    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
365    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
366    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
367    
368    checkpoint52d_post
369    o re-tiled many expts to allow comparison in multi-processor mode
370      - updated output accordingly
371      - changed hs94.128x64x5 to use intial T from file rather than use the
372        random number generator
373    o add infrastructure in model routines for fizhi and gridalt packages
374    o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
375    o changes to permit hi-res, cubed-sphere, configuration
376      - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
377      - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
378      - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
379        of surface winds for the cube
380      (A verification experiment, based on global_ocean.cs32x15, but with
381       pkg/seaice turned on and with on-the-fly interpolation from the NCEP
382       Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
383       complete with example surface forcing files and matlab scripts to look
384       at the output and compare it with that of global_ocean.cs32x15.)
385    o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
386       but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
387       to conform to the common rule.
388    o check-in the first version of the coupler + interfaces for multi-components
389       set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
390       - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
391       - atmosphere: use pkg aim_v23 ; no sea-ice for now.
392       - ocean and atmos. share the same horizontal grid (no interpolation).
393       - exchanges between component and coupler is done in forward_step
394    o new verification experiment, cpl_aim+ocn:
395       coupled ocean - AIM atmosphere on cs32 grid.
396    
397    checkpoint52d_pre
398    o surface flux time-av diagnostic modified for NLFS & RealFreshWater
399    o add call to AIM pendant S/R in external_forcing & external_fields_load.F
400    
401    checkpoint52c_post
402    o Fixing OPTIONS files for use of exf:
403      - ALLOW_ECCO not needed
404      - ECCO_CPPOPTIONS.h should not be included from
405        EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
406        as has been the case in the past
407      - All cal/exf related options are currently set in
408        single header file. Should remain so until we
409        agree on a consistent new policy.
410    o Removed all CPP options for cal package.
411      cal has no more CPP options.
412    o modified STOREs in GAD_ADVECTION
413    o corrected key comp. for passkey
414    
415    checkpoint52b_post
416    o new version: "thsice" of thermodynamic sea-ice pkg:
417     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
418     - modify fluxes but do not change theta directly;
419     - light cleaning of bulk_force pkg (still needed with thsice).
420     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
421       + output_thsice.txt to test thsice & bulk_force pkgs.
422    o put back grid & coriolis monitor output.
423    checkpoint52b_pre
424    
425    o call "do_the_model_io" at the beginning (=> dump initial state)
426    o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
427    o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
428      (need info on NUMBER_OF_PTRACERS)
429    o missing PTRACERS headers in some routines
430    o default tamc.h in pkg/autodiff supposed to crash
431      to ensure proper customization
432    
433    checkpoint52a_post
434    o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
435      - moved surfaceTendencyTice from pkg/seaice to main code
436      - subroutine FREEZE_SURFACE now limits only surface temperature
437        and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
438        => new output.txt for global_ocean.cs32x15 & global_with_exf
439      - keep the old version of FREEZE for backward compatibility;
440        global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
441      - corresponding modifs for TAF directives
442    o added surface flux output variables to TIMEAVE_STATVARS
443    o time-averaged output for pkg/ptracers
444    o fix problem with ECCO-related divided adjoint
445      snapshot file was missing some ad-variables,
446      but no warning issued by TAF
447    
448    checkpoint52a_pre
449    o some bug fixes for #undef REAL4_IS_SLOW
450    
451    checkpoint52 = ecco_c52_e35
452    o after testing adjoints of checkpoint51u_post
453    
454    checkpoint51u_post
455    o this is the post-merge tag of the ecco-branch
456      (needs another clean checkout and re-testing)
457    o various natl_box_adjoint configs and results
458      but no input fields
459    o obcs adjoint not yet merged!
460    o adding ECCO global 1x1 and 2x2 degree configs
461    o updated/extended some store directives for seaice
462    o pkg/ecco now containes ecco-specific part of cost function
463    o top level routines the_main_loop, forward_step
464      supersede those in model/src/
465      previous input data.cost now in data.ecco
466      (new namelist ecco_cost_nml)
467    o in ctrl/ cleaned some cross-dependencies and updated CPP options
468    
469    checkpoint51t_post
470    o this is the pre-merge tag of the ecco-branch
471    
472    checkpoint51s_post
473    o cleanup: removed various obsolete #define-s
474    o pkg/grdchk
475      - renamed 'ph-grd 3' to 'grad-res'
476      - merged from ecco-branch
477        (remaining bug fixes for obcs gradient checks)
478      - additional high-precision output for testreport
479        (grep for 'precision_grdchk_result')
480    
481    checkpoint51r_post
482    o cleaned up or removed CPP_OPTIONS.h files
483    o updated results for some of the tests to reflect the new
484      optfiles (-ieee: -O0 instead of -O3)
485    
486    checkpoint51q_post
487    o cd_code:
488      - moved cd_scheme.F -> cd_code_scheme.F
489      - separate read_checkpoint from cd_code_ini_vars.F
490      - separated cd_code part from write_checkpoint
491      - updated AD_SOURCE, generated .flow
492      - added CD_CODE_VARS.h to the_main_loop
493      - Moving cd_code specific store dir.s to pkg/cd_code
494    o ctrl package totally restructured
495      - pack/unpack now optional and decoupled from
496        xx_/adxx_ I/O
497      - ctrl_pack/unpack cleaned
498        (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
499      - confined inclusion of AD_CONFIG.h to where necessary.
500    o genmake2: changed AD dependencies from SRCFILES to AD_FILES
501    
502    checkpoint51p_post
503    o create initial cd_code package
504      - WARNING: the initialization of fields within packages
505        is broken because INI_FIELDS (where READ_CHECKPOINT is
506        called) is called *before* PACKAGES_INIT_VARIABLES.
507        This seems to be backwards since
508        1) its important to initially zero the entire field including
509           the "halo" region
510        2) zeroing needs to be done *before* reading pickup info
511           and the pickup call might or might not happen in any
512           particular run
513      - this needs an overhaul for R2
514    o cleanup verification/*/code/GMREDI_OPTIONS.h
515    o cleanup testreport
516    
517    checkpoint51o_post
518    o bringing AD-related verif's up to date with genmake2
519      - carbon/
520      - global_ocean.90x40x15/
521      - hs.94.1x64x5/
522      - (front_relax/ )
523    o (more) consistent directory structure for AD-related verif.'s
524    o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
525    o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
526    o bug fix in find_alpha.F for MDJWF:
527      - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
528        change rho -> rho-rhoConst
529      - replace call find_rho to find_rhonum
530    o initialisation of rFlx extended to full array (required by TAF)
531      and shifted to thermodynamics
532    o removed PTRACERS.h in ptracers routine
533    o added surfacetendencyPtr to S/R parameter list pracers_forcing
534    o Correcting initialisations for fVerU, fVerV.
535    o helping TAF to recognize dependency on kUp for
536      fVerU, fVerV
537    o Replacing delZ by delR in pkg/ctrl/
538    checkpoint51o_pre
539    
540    o undid all of cp51 pending some cleanups and discussion
541    o added the [#include "AD_CONFIG.h"] statement to all files that need
542       it for adjoint/tl #defines
543     o re-worked the build logic in genmake2 to support AD_CONFIG.h
544     o removed tools/genmake since it no longer works
545    
546    checkpoint51n_post
547    o modifications to make FREEZE flux visible to pkg/kpp
548      - moved surfaceTendencyTice from pkg/seaice to main code
549      - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
550      - subroutine FREEZE now limits only surface temperature
551        (this means new output.txt for global_ocean.90x40x15,
552         global_ocean.cs32x15, and global_with_exf)
553    o added surface flux output variables to TIMEAVE_STATVARS
554    
555    checkpoint51n_pre
556    o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
557    o added [#include "AD_CONFIG.h"] to all files that use the following
558      defines:
559      - ALLOW_ADJOINT_RUN
560      - ALLOW_TANGENTLINEAR_RUN
561      - ALLOW_ECCO_OPTIMIZATION
562    
563    checkpoint51m_post
564    o incorporating changes to get TAMC/TAF working in genmake2
565      - added new TAMC/TAF targets to the Makefile
566      - various cleanups related to package handling
567      - these changes should have no impact on the forward model
568    
569    checkpoint51l_post
570    o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
571     - faster algorithm for cal_addtime.F
572     - higher precision arithmetic, where needed
573     - pkg/exf *startdate variables changed from calendar date to
574       model integration time
575    
576    checkpoint51l_pre
577    o add salt flux to forcing fields (used when salty sea-ice forms or melts)
578    o enable to apply restoring on S & T only in a latitude band.
579    o update output (external_forcing_surf modif. change truncation errors)
580       global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
581    
582    checkpoint51k_post
583    o change default to: useNHMTerms=.FALSE.
584     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
585       adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
586     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
587        exp1, ideal_2D_oce
588     - change data file of oceanic exp (leave the results unchanged for now)
589       exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
590    o set gravitySign automatically according to the vertical coordinate used
591      (and change sign: back to "logical" value: +1 when R increases downward)
592    o added an include barrier to the default CPP_OPTIONS.h and
593      removed the #include "PACKAGES_CONFIG.h" from it
594    o fix a bug in mom_fluxform (from chk51j_post)
595    
596    checkpoint51j_post
597    o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
598    o adjusted some flow directives (dynamics, thermodynamics)
599    o added cubed-sphere case to test cost function
600    o heckpoint_lev?_directives.h now include
601      pkg-specific directives, whenever those are enabled.
602    o Moving pkg-specific flow directives to corresponding pkg
603      Moving pkg-specific differentiation list to corresponding pkg
604      Moving pkg-specific checkpoint-lev storing to corresponding pkg
605      ---> conventions are
606           - pkg_ad.flow
607           - pkg_ad_diff.list
608           - pkg_ad_check_lev?_dir.h
609    
610    checkpoint51i_post
611    o merge of the branch-genmake2
612      - knowingly breaks the older genmake
613      - automatic generation of all ALLOW_${PKG_NAME} defines
614      - new testreport supersedes older testscript
615    o large number of package inclusion and header cleanups
616    checkpoint51i_pre
617    
618    o new output for adjoin of global ocean vector invariant
619    o fix for checkpoint of thermodynamic seaice and bulk_force
620    o Steph gchem various cleanups
621    
622    checkpoint 51h_pre
623    o fixed some single quotes
624    o modify gchem pkg to be more versatile
625    o modifications to clean up dic pkg
626    o add pkg/cfc
627    
628    checkpoint51g_post
629    o provide links for ARPACK and ADM*TLM
630    o start removing verification/vero/
631    o update AD-related stuff
632      (in particular some IF-statements in model/src/ routines)
633    o adding to verification/global_ocean.90x40x15/ adjoint of
634      vector invariant setup
635    
636    checkpoint51f_post
637    o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
638    o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
639      of tracer Green's fucntions for ocean inversion project.
640    
641    checkpoint51f_pre
642    o Added on-the-fly spatial interpolation capability
643        "USE_EXF_INTERPOLATION" to pkg/exf.
644      - This is a temporary Cartesian-grid hack until
645        the super-duper ESMF coupler becomes available.
646      - See verification/global_with_exf/README for usage example.
647      - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
648        flags and modified pkg/seaice accordingly.
649    o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
650        and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
651        non-local transport term.
652    
653    checkpoint51e_post
654    o pkg/mom_vecinv:
655      - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
656      - add time-ave diagnostic of vorticity advection.
657    o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
658    o atmospheric geopotential: - include water vapor effect;
659                                - use p^kappa in p* scaling.
660    o land pkg: read initial state from files.
661    o AIM : add stratospheric drag in the upper level
662    
663    checkpoint51d_post
664    o change function ILNBLNK (=> last non-blank char.) to return zero
665      (instead of the string length) when the string. char is empty
666    o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
667    o modif's to restore TAMC compatibility
668      - avoid "_d" constructs in PARAMETER declarations
669      - avoid interrupting lines by comment lines
670    o Use cluster local disks for purely local I/O
671      vs. globally visible disks needed for ctrl stuff
672      (merged from ecco-branch)
673      - new active_file_loc... and mdsio_..._loc routines
674      - affected packages: autodiff, ctrl, grdchk, mdsio
675    
676    checkpoint51c_post
677    o introducing integer flag debugLevel
678      - debLevZero: suppress all output
679      - debLevA: standard
680      - debLevB: equivalent to current debugMode=.TRUE.
681    o introducing pathname variable mdsioLocalDir for mdsio
682      that can be specified at runtime
683      (relevant for cluster I/O to local disk)
684    `
685    >>>checkpoint51b_post
686    adjoint of ptracers
687    o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
688    o extended state in checkpoint_lev?, etc.
689    o alternative ctrl/cost with tr1 or ptracer
690    o new comlev1_bibj_ptracers
691    o new ptracers.flow
692    o made ptracers_forcing same as external_forcing_s
693    o added verification for adjoint with ptracers
694      - adm. grdchk fail so far
695      - tlm. grdchk OK
696      - checked tapelev/comlev recomputations: OK
697    <<<checkpoint51b_pre
698    
699    checkpoint51a_post
700    o added code for biogeochemistry package
701      - new pkgs: dic, gchem
702      - new subroutine in ptracers
703    o modify code for biogeo packages
704      - in model/src and pkg/ptracers
705    
706    checkpoint51
707    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
708      - autodiff, ctrl, exf, grdchk, seaice
709      kept separate packages
710      - cost, ecco, obcs
711    o updating verification/internal_wave, verification/lab_sea
712      (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
713    
714    checkpoint50i_post
715    o Preparing next differentiable checkpoint and sync
716      of MAIN vs. ecco-branch
717      - 1st step: this one is differentiable
718      - 2nd step: next(! not this) checkpoint will have updated packages
719                  from ecco-branch)
720    
721    checkpoint50h_post
722    o new package "land": provide surface BC for AIM.
723    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
724    o AIM: use true log-P extrapolation for near surface temp (= as in
725        F.Molteni paper) ; update aim.5l_cs output.
726    o New variable in PARM03 for more flexible pickups
727    o somewhat cleaned package initialisation sequence for
728      ctrl/ cost/ ecco/ in packages_... routines
729    
730    checkpoint50g_post
731    o merged with release1_p17 (pkg/seaice and verification/lab_sea)
732      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
733      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
734        made the default because of faster convergence than ADI
735    
736    checkpoint50f_post
737    o exf totally restructured
738      - replaced all exf_set_ routines by one generic exf_set_gen.F
739        and made sure it's still differentiable
740      - split exf_getffields.F into new exf_bulkformulae.F
741      - exf_inscal_/exf_outscal_ suffixes consistent with field names
742      - updated adjoint/makefile and relevant verif. accordingly
743    
744    checkpoint50f_pre
745     o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
746          + change Evap over land. (update aim.5l_cs output)
747     o added missing .cvsignores and made uniform across expts
748     o changed configuration of tidal_basin_2d expt
749     o added pkg/debug functions for tracing code in fatal crashes
750     o tidied pkg/monitor to use MONITOR_OPTIONS.h
751     o new fn in pkg/monitor to stop model if solution grows too big
752     o removed lots of single quotes from comments
753    
754    checkpoint50e_post
755    o make KPP work with PTRACERS
756     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
757       nearly a copy of kpp_transport_s
758     - there is no analogue to SurfaceTendencyS, so I have to use
759       gPtr(of the surface layer) instead
760    o add a new platform SunFire+mpi (SunFire 15000) to genmake
761    checkpoint50e_pre
762    
763    checkpoint50d_post
764    o change kpp output from multiple-record state files to single-record state
765      files analogous to write_state.F
766    o reduce the output frequency of cg3d-related stuff to the monitor frequency,
767      analogous to the cg2d-related output.
768    o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
769      so that writing to internal file fn (with length 512) fails.
770    checkpoint50d_pre
771    
772    checkpoint50c_post
773    o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
774    o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
775    o add time-average diagnostic of U*V and vertical diffusive flux for theta.
776    o bug fixed in convective adjustment diagnostic (multi-tile set-up).
777    o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
778    
779    checkpoint50c_pre
780    Merging from release1_p13:
781    o bug fix for pkg/seaice dynamic solver
782    o Added SEAICE_initialHEFF to pkg/seaice
783    
784    checkpoint50b_post
785    o store u*,v* in gU,V instead of in guNm1,gvNm1
786    o in order to put the momForcing out of the Adams-Bashforth:
787      move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
788      to timestep.F
789    o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
790    o re-generate output for highly sensitive test-exp:
791       global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
792    
793    checkpoint50b_pre
794    o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
795    o corrected CPP option mismatch in exf_Bulk... functions for case
796      #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
797    
798    checkpoint50a_post
799    o Bug fix for merging between c50 and KPP.
800      ikey was passed from thermodynamics to kpp_calc via
801      common block rather than being recomputed in kpp_calc,
802      in contradiction with new key itdkey.
803      New key ikppkey created, and tamc.h headers updated.
804    
805    checkpoint50
806    - 2nd step of merge with ecco-branch:
807      merge changes in ecco-branch back into main trunk
808    - bug fix in find_alpha
809    - more storing in gmredi_calc_tensor.F, kpp_routines.F
810    - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
811    - merged some sliced AD support routines
812    
813    checkpoint49
814    merged from ecco-branch:
815    o exf:
816      - Enable initialisation of forcing fields to constant
817        (runtime) values.
818      - in exf_getffields.F
819        Reduce i-/j-loop to interior domain, discarding overlaps.
820        That also fixes wrong TAF-key computations for key_1, key_2
821        with bulf formulae.
822      - exf_init.F modify #ifdef for exf_init_evap
823      - exf_getffieldrec.F, ctrl_getrec.F
824        The following INT-usages are not safe:
825          fldsecs  = int(fldsecs/fldperiod)*fldperiod
826          fldcount = int(fldsecs/fldperiod) + 1
827        and were modified.
828    o autodiff: checkpoint_lev...
829      - updated storing for bulk formulae (some arrays were missing)
830      - added state for seaice package
831      - synchronized with main branch
832    o DIVA:
833      Modif.s in
834      - the_main_loop.F
835      - the_model_main.F
836      and added cost_final_restore.F cost_final_store.F
837      o With these changes, it is possible to fully separate
838        the first forward run to compute the cost function (mdthe_main_loop)
839        and adjoint runs over individual DIVA intervals (adthe_main_loop)
840        into separate model executions.
841        This enables better tuning of DIVA to given queue sizes.
842      o Loss of cost function value in consecutive DIVA runs is
843        fixed by storing to 'costfinal' file.
844      o Appropriate call of ctrl_unpack/_pack,grdchk_main at
845        beginning/end of adjoint integration is accounted for.
846      The current changes apply to TAF-1.4.26.
847      TAF has one remaining bug, requiring one manual change
848      (see MITgcm manual).
849    o cal: synchronized between MAIN and ecco-branch
850    
851    checkpoint48i_post
852    o Changes to restore differentiability of code w.r.t. previous tag
853      (mostly adding new routines to make list and replacing
854      pressure by totPhiHyd).
855    o Updated and merged grdchk package
856      - has both ADM and TLM checks
857      - works for single- and multi-proc.
858      - output cleaned
859      - worked successfully for parallel DIVA
860    o genmake:
861      - Adding -platform=SP4
862      - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
863    o Modif. for DIVA:
864      ctrl_unpack should not be called in intermediate DIVA interval.
865      (similar thing would apply for active files such as
866      tbar, sbar, psbar, which should not be reinitialised;
867      only relevant for ecco-branch)
868    
869    checkpoint48h_post
870    o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
871    o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
872    o Added SEAICE_initialHEFF to pkg/seaice
873    o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
874    
875    checkpoint48g_post
876    --- EOS:
877    o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
878      store total Potential in totPhyHyd for diagnostics & EOS.
879    o fix restart and overlap Pb when using Z-coord and EOS funct. of P
880    --- Pressure/geopotential gradient:
881    o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
882    o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
883      ( changes results of global_ocean_pressure )
884    o NLFS + z-coord.: add eta*Rho' contribution.
885    o accurate phiHyd when using interface-W at the middle between 2 centers
886     ( changes results of ideal_2D_oce )
887    o includes r* 2nd term in potential gradient.
888    
889    checkpoint48f_post
890    Merging from release1_p12:
891    o Modifications for using pkg/exf with pkg/seaice
892      - improved description of the various forcing configurations
893      - added basic radiation bulk formulae to pkg/exf
894      - units/sign fix for evap computation in exf_getffields.F
895      - updated verification/global_with_exf/results/output.txt
896    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
897      (SBO) core products, including oceanic mass, center-of-mass,
898      angular, and bottom pressure (see pkg/sbo/README.sbo).
899    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
900      to avoid negative values in shallow regions.
901      - updated verification/natl_box/results/output.txt
902      - updated verification/lab_sea/results/output.txt
903    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
904    o Added useSingleCpuIO option (see PARAMS.h).
905    o Updated useSingleCpuIO option in mdsio_writefield.F to
906      work with multi-field files, e.g., for single-file pickup.
907    o pkg/seaice:
908      - bug fix in growth.F: QNET for no shortwave case
909      - added HeffFile for specifying initial sea-ice thickness
910      - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
911    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
912      kpp_transport_t.F, forward_step.F, and the_main_loop.F
913    o pkg/seaice:
914      - adjoint-friendly modifications
915      - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
916    
917    checkpoint48e_post
918    o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
919    o dynamics: change definition of computational domain & adapt mom_fluxform
920      accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
921    o following exp works with Olx=Oly=2 (and pass through checkbounds option):
922        adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
923        exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
924        global_ocean.90x40x15 global_with_exf global_ocean_pressure
925        inverted_barometer solid-body.cs-32x32x1
926      (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
927    
928    checkpoint48d_post
929    o in preparation for r*:
930     a) use pre-computed gradient of hydrostatic potential:
931        changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
932     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
933        => affects results of glob_oce_pressure (different truncation error)  
934      update output.txt of ideal_2D_oce & global_ocean_pressure
935    
936    checkpoint48d_pre
937    o in preparation for r*:
938      new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
939      pass the 2 comp. of the grad. as arguments to momentum S/R.
940      but for the moment, only used if it does not change the results.
941    o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
942    
943    checkpoint48c_post
944    Modifications in treatment of initial flux forcing controls
945    to avoid extra storing of flux fields.
946    
947    checkpoint48c_pre
948  o Added tidal_basin_2d experiment (currently 1D!)  o Added tidal_basin_2d experiment (currently 1D!)
949  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)
950    
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