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revision 1.390 by jmc, Sun Nov 21 22:22:31 2004 UTC revision 1.610 by mlosch, Wed Feb 15 08:59:48 2006 UTC
# Line 1  Line 1 
1  $Header$  $Header$
2    $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint58a_post
8    o shelfice:
9      - separate shelfice load anomaly from pload (breaks with time
10        dependent forcing), => introduce constant field shelficeLoadAnomaly.
11        Its default is 0., but it may be computed more cleverly from (unknown)
12        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
13        done offline. A good approximation of the pressure load anomaly is
14        necessary to avoid large initial adjustment processes underneath
15        deep-reaching shelfice.
16      - small fix in ISOMIP shelfice_thermodynamics
17      - add more sophisticated thermodynamics of Hellmer (1989), this is
18        now the default
19      - give a few constants more intuitive names
20    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
21      if bulk formulae are used in long integration (especially EmPmR). Turn
22      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
23      if balancePrintMean, the imbalance that is substracted is printed to
24      STDOUT.
25    o fix bug (typo) in obcs_apply_eta.F
26    o add a new package shelfice which enables us to model the circulation
27      underneath shelf-ice with draughts of hundreds of meters.
28     - works
29     - to do: + include improved thermodynamics
30              + check whether kSurfC (from model/inc/SURFACE.h) can be used
31                instead of new field kTopC
32              + can we use topoFile, Ro_surf and existing code in ini_depth.F
33                instead of new field R_shelfIce and new code in ini_depth.F
34                and ini_mask_etc.F?
35              + adjust vertical mixing schemes?
36    o seaice pkg:
37     - add a cpp-flag to include a simple formula for a salinity dependent
38       freezing point of sea water at the surface
39     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
40       meridional stresses are now different (and hopefully correct)
41    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
42       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
43       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
44    o pkg/diagnostics: add options and parameters for regional-statistics
45       diagnostics ; define regions by reading a region-mask from a file
46       (might add other options later)
47    o pkg/bulk_force:
48     - add option and parameters to use AIM surface-flux formulae.
49     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
50       others forcing fields (defined in PARM05, parameter file "data") are loaded
51       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
52     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
53     - use the right EXCH call for uwind,vwind (to work on CS-grid).
54     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
55       and parameters (note: calcWindStress replaces .NOT.readwindstress).
56     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
57    
58    checkpoint58
59    o add "--embed-source" option to genmake2 which, when the supporting
60      tools can be compiled (as determined by genmake2) will turn on the
61      embed_files package which then embeds the entire MITgcm source code
62      (*.[fFhc] + Makefile) used for the build within the executable
63      - requested by CNH but off by default
64      - adds a paltry <9MB to the mitgcmuv executable in most cases
65      - only writes the output when useEMBEDSRC in eedata is true
66    o clean up 3-dim. relaxation codes:
67      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
68      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
69      * Thanks to Tom Haine for testing!
70    
71    checkpoint57z_post
72    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
73      affects output (@ truncation level) of exp. plume_on_slope ; updated.
74    o fix the pickup behavior for obcs in combination with ptracers
75    o fix a bug in ptracers_external_fields_load
76    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
77      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
78    o transfered surface NH pressure to eta field (if exactConserv).
79    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
80         and update lab_sea output.txt file.
81    o completing 3-dim. relaxation code: additional term
82         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
83      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
84      * At compile time, in "EXF_OPTIONS.h" set
85          #define  ALLOW_CLIMTEMP_RELAXATION
86          #define  ALLOW_CLIMSALT_RELAXATION
87      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
88          tauThetaClimRelax3Dim = 15552000.0,
89          tauSaltClimRelax3Dim  = 15552000.0,
90      * 3 cases:
91          1) Use a constant-in-time 3-dim. field
92          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
93          3) Real-time relax. to time-evolving prescribed field
94    o Adding Laplacian-type smoothness constraint on
95      initial and boundary (forcing) controls (ic, bc)
96      * enable at compile-time via
97        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
98      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
99      * Absolute scale somewhat unclear so far
100      * no area weighting was included since no other cost term does so far
101    
102    checkpoint57y_post
103    First step for a NLFS adjoint
104    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
105    o new init. routines for calc_r_star, calc_surf_dr
106    o still need to deal with ini_masks_etc
107    o testreport seemed happy
108    checkpoint57y_pre
109    
110    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
111    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
112    o add new offset feature to offline pkg (plus minor cleanup)
113    o cfc fixes for final year of integration
114    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
115      be in GCHEM_OPTIONS).
116    
117    checkpoint57x_post
118    o fix testreport Pb in multiple test experiment.
119    o cleanup our namelist syntax in verification:
120      - make it more F95 standards compliant (some work still needed)
121      - allows the vast majority of our tests to work with gfortran
122    o Non-Hydrostatic:
123     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
124     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
125    o Allow to apply AB on T,S rather than on AB(gT,gS):
126     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
127     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
128       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
129     - need a "clever" read_pickup to restart from the other AB formulation
130    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
131    o remove some unused variables (reduces number of compiler warnings)
132    o adjoint
133      * Disable useVariableViscosity for adjoint for time being
134        (there are a number of extensive recomputations)
135      * Initialize certain variables needed for adjoint
136    
137    checkpoint57w_post
138    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
139                 fix the singleCpuIO RS version of MDSWRITEFIELD
140       and add a WARNING if using globalFiles=T with multi-processors.
141    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
142      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
143    o tracer advection scheme:
144      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
145       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
146       was not very convenient).
147      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
148       (further tests needed for the implicit DST & Flux-Limiter schemes).
149    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
150      and sRef for convenience, handy, when you want to initialize
151      ptracers in a large domain with a constant non-zero value. Also,
152      untangle ptracers_init.F a little.
153    
154    checkpoint57v_post
155    o change dome exp. to use variable viscosity in side-drag terms.
156    o remove all the files from the cfc_offline test since they are now
157      incorporated into tutorial_cfc_offline which has been producing
158      identical results for a few days of testing
159    o add new parameter: sideDragFactor to enable half-slip-side BC
160      and change side-drag S/R to use viscosity from mom_calc_visc
161      (can switch back by setting sideDragFactor=0.); affects results at
162      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
163       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
164    o vorticity & strain are now computed without masking, to account for
165      no-slip-side BC in variable viscosity calculation ; mask is applied
166      anyway later on, before computing advection/coriolis terms.
167    o modify exp4 to test new obcs support for reading from external files
168      and for passive tracers
169    o fix behavior of ptracers_monitor when monitor output is written to a
170      netcdf-file; still not independent of monitor.F (writes in the same
171      file).
172    o change default value of tRef (put a uniform, meaningful value for ocean
173      & atmos) and initialize sRef (was missing, as Martin mentioned).
174    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
175      to be proportional to enstrophy dissipation length.  Thus,
176       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
177      This is now consistent with Smagorinsky and with the manual.
178    
179    checkpoint57u_post
180    o OBCS and PTRACERS: add open boundary support for passive tracers
181      - either use homogenous (pseudo) v.Neumann conditions or prescribe
182        OB-values from file; this is not different from the way theta and salinity
183        are treated
184      - however, Orlanski-radiation conditions are not supported, and the model
185        will stop if you use pTracers and Orlanski at the same time.
186      - beefed up the rountine obcs_external_fields_load: now only those open
187        boundary values are overwritten with values from files for which there
188        are really files, otherwise the OB-fields remain untouched. This makes
189        it possible to use different OBs at different ends of the domain (as
190        with EXF)
191    o reduce number of exch calls in shap_filt (s2).
192    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
193      truncation level) 4/5 MLAdjust test results (11&12 digits match).
194    
195    checkpoint57t_post
196    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
197    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
198      same truncation, independent of the face number: affects affects several
199      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
200    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
201      note that biharmonic viscosity + no-slip was not tested in any experiment.
202    o fix bug in non-linear free-surf side-drag ; generate new output for
203      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
204    o make mnc honor the writeBinaryPrec flag for most kinds of output
205    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
206    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
207      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
208    o add brackets in multi-terms sum to get same truncation, independent of
209      the face number (manage to get exactly same value of gU,gV at the cs-edge)
210      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
211    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
212      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
213      a maximum grid-scale Reynolds number.  Also, changes all length calculations
214      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
215      Suggested values of viscosity parameters found in mom_calc_visc.
216      Many new viscosity diagnostics available.
217    
218    checkpoint57s_post
219    o Add clearing-house for viscosity calculations, mom_calc_visc and
220      correct numerous bugs in LeithD and Smagorinsky discretizations.  
221      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
222      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
223      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
224      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
225      The Strain-Tension form is now called with useStrainTensonVisc=.true.
226      ViscAhStrain and viscAhTension are now retired.
227    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
228    o In response to JMC's bug report, genmake2 now ignores any soft-links
229      that it finds in the *current* directory when searching for files.
230      Soft-links found in any other source directories will still work as
231      they did before.
232    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
233      a C routine to unlimit the stack size
234    o mnc-ify pkg/aim snapshot vars
235    o mnc-ify pkg/land as requested by Daniel
236    o various changes to mnc including:
237      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
238      - output can now be grouped so that all files within a group
239          change the ITER portion of their names in lock-step together
240      - can now read ("global") PER-FACE (in addition to PER-TILE) files
241          and works with both EXCH1 and EXCH2 (but needs more testing)
242      - writing works for all verification test cases w/ g77 on Linux
243    
244    checkpoint57r_post
245    o make MNC variable initialization happen earlier
246    o add diagnostics for (almost) each term of the momentum Eq.
247    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
248    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
249    o remove MINIMAL_TAVE_OUTPUT option ;
250      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
251    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
252      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
253    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
254    o add time-dependent SST, SSS control
255    o cost terms in ecco/ modularized (new cost_generic.F)
256    o cost_averages routines are modularized (new cost_averagesgeneric.F)
257    o new infrastructure for seaice model vs. obs misfits in seaice/
258      * driver from the_main_loop.F is seaice_cost_driver.F
259      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
260      * gradient check in Exp. 6a of natl_box_adjoint/
261    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
262      (see README file)
263    
264    checkpoint57q_post
265    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
266    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
267      - bug was reported by Jean-Michel and Ian Fenty
268    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
269      update exp. cpl_aim+ocn output.
270    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
271      Needed for high-res. runs with large global files
272      to be able to limit tapelev size
273    o Changed some tests for adjoint:
274      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
275      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
276      * global_ocean.90x40x15/ back to default 3-level checkpointing
277    o Modifications to enable scripted COMMON to MODULE conversion
278      * verification/OpenAD/code/ has necessary scripts and description;
279      * converts, compiles and runs successfully;
280    
281    checkpoint57p_post
282    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
283    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
284      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
285    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
286    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
287      (was already the case for dissipation with mom_vecinv,
288       and also the case for grad.PhiHyd when staggered-timeStep)
289      This will allow to put dissipation out-off the AB time-stepping.
290     Unfortunately, affects truncation error. Update output of exp. that "fails"
291      (cg2d matching number) and leave the others for later: front_relax(10),
292      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
293      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
294    
295    checkpoint57o_post
296    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
297      (2) its ready to be documented during the 20050801 DocFest
298    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
299      for ideal_2D_oce and lab_sea on linux_ia32_g77
300    o set to #undef CTRL_SET_OLD_MAXCVARS_30
301      in global1x1_tot/code_seaice_adj to access indices 32, 33
302      (worth another tag)
303    
304    checkpoint57n_post
305    o adding precip control xx_precip 32
306    o adding swflux control xx_swflux 33
307    o Replacing 10 forcing penalty cost routines by 1 generic.
308    o Implementing partitioning in time-mean and variable adjustment
309      for atmos. state.
310    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
311    o in natl_box_adjoint:
312      * updated exp 1 to 10
313        (but does not have time-mean vs. variable split results yet)
314    o updated global1x1/*_seaice_adj/
315      to incorporate latest changes
316    o enable useSingleCpuIO for mdsio vector routines
317      (applies in particular to tapelev I/O)
318    o removed inefficient K-loop in all active_file*control*.F
319    
320    checkpoint57m_post
321    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
322      and advect_cs (use EXCH-2 and standard cs-32 grid files).
323    o pkg/exch2: filling of face-corner halo regions is optional
324      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
325    
326    checkpoint57l_post
327     tag before updating tutorials (pre-release-2)
328    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
329       for output and interpolation of input fields onto model grid)
330    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
331       Affects results of exp. rotating_tank ; update output.txt.
332    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
333          and taking the square quantity and/or using a fraction-weight field.
334    o fix aim_diagnostics_init.F mate numbers.
335    o add mnc output capability to diagnostics/diagstat and update
336      our cvsignore files for the ACSII output generated
337    
338    checkpoint57k_post
339    o lab_sea now uses diagnostics package and provides a suite of
340      new EXF diagnostics output.
341    
342    checkpoint57j_post
343    o exf
344      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
345        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
346        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
347      * extended diagnostics output
348        - now includes all EXF variables
349        - hs, hl moved to common block
350        - separate S/R for diagnostics, called after ctrl vector is added
351        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
352        - EXFqnet contains true Qnet (i.e. includes qsw)
353      * updated verif. lab_sea, global_with_exf
354      * Rearranging hflux (exf_mapfields -> exf_getforcing)
355        to ensure that diagnostics sees a true EXFqnet
356    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
357    o diagnostics pkg: change pointers so that 1 diagnostic can be used
358      several times with different frequencies.
359    o mnc-ify the thsice package as requested by Daniel Enderton
360      - the monitor--MNC output needs work
361      - many attributes need to be added (most are currently blank)
362    o mnc-ify theaim_v23 package as requested by Daniel Enderton
363      - many attributes need to be added (most are currently blank)
364    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
365    o add Sadourny like discretization to the 4th.O vorticity advection scheme
366    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
367      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
368         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
369    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
370     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
371    
372    checkpoint57i_post
373    o Diagnostics package was changed: diagnostic allocation is now deactivated
374      by setting an empty file name in the namelist (used to be by setting 0 frequency)
375    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
376      add 1rst Order upwind vertical Shear.
377    o add a quick fix for A/B checkpointing in OFFLINE mode
378    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
379      end-run around the C/Fortran linking horror in eesup/src/timers.F
380    o added pkg/runclock: allows user to terminate run based on wall clock
381    o added non-hydrostatic scaling parameter: nh_am2
382    o pkg/my82: futile attempt to make results compiler-independent by adding
383      some "_d 0", etc. no effect.
384    o for mnc output, fill the 'T' coordinate var with myTime and create a
385      separate 'iter' variable for iteration count
386    o pkg/diagnostics:
387      add new capability: output of Global/Regional & per-level statistics ;
388      tested against monitor output (including land & thSIce) on various exp.
389    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
390    
391    checkpoint57h_done
392      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
393      data.diagnostics, data.gchem, data.ptracers) is done.
394    
395    o pkg/diagnostics: prepare for Global/Regional statistics.
396      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
397    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
398      and rename it: DIFFERENT_MULTIPLE
399    
400    checkpoint57h_post
401    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
402    o pkg/diagnostics: change output frequency, now in seconds (instead
403      of Nb of iterations). This requires to change data.diagnostics.
404    checkpoint57h_pre
405    
406    o in mnc, let the user create the output dir if both mnc_outdir_date
407      and mnc_outdir_num are false
408    o add fflags() to pkg/diagnostics which allows one to specify, on a
409      per-file basis, the file precision [default behavior is unchanged]
410    o added diagnostics to pkg/kpp, including computation of mixed layer
411      depth based on a temperature/density criterion
412    o updated verification/natl_box to test the new pkg/kpp diagnostics
413    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
414    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
415    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
416      not mnc -- this mistake was found by JMC and is now corrected
417    
418    checkpoint57g_post
419    o add Adams-Bashforth 3rd Order time stepping:
420      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
421      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
422    checkpoint57g_pre
423    
424    o make lambda[Theta,Salt]ClimRelax spatially varying
425      (default remains spatially uniform constant based on tau)
426    o added new control variables
427      * init. uVel, vVel, etanN
428      * lambda[Theta,Salt]ClimRelax
429    o separate masks used for ctrl_pack/unpack 'from write_grid' output
430      (suggested by G. Forget)
431    
432    checkpoint57f_post
433    o add parameter "baseTime" = model base time = time at iteration zero
434      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
435      account for baseTime shift
436    o move Coriolis arrays from PARAMS.h to GRID.h
437    checkpoint57f_pre
438    
439    o mnc-ifying the seaice package
440    o introduced an alternative length scale calculation for use in the limiting
441      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
442    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
443    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
444      as well as grad(vort3).  Made it compatible with both approximate form
445      for the cubed sphere and full form of these gradients.  Added flag
446      useFullLeith to select between approximate and full form.  
447    o add "d0" in getcon.F to reduce differences between compilers/platforms
448      update output.txt of exp. fizhi-gridalt-hs
449    o change port_rand funtion to allow to set the seed.
450    o fix obscure MNC bug involving conversion between reals and integers
451      - it caused no problems with certain (eg. gcc, ifc) compilers but the
452        new version is now more standards-compliant
453    o adjoint-related modifications
454      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
455      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
456      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
457    
458    checkpoint57e_post
459    o Adding eddy stress controls a la Ferreira et al.
460    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
461    
462    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
463      update output.txt of exp. fizhi-gridalt-hs
464    o add more "Z" dimensions and associated coordinate vars to MNC
465    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
466    o parameter calendarDumps: when set, approximate months (30-31 days) and years
467      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
468      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
469      months and years.  Requires pkg/cal.
470    o diagnostics: add pickup functionality
471      - off by default for backwards compatibility
472      - current version only uses MDSIO -- MNC will be added
473    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
474    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
475    
476    checkpoint57d_post
477    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
478    o modify verification/ideal_2D_oce so that it tests the creation of mnc
479      output from the diagnostics package
480    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
481    o make genmake2 more portable by using ".$FS" instead of ".f" for more
482      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
483    o add coordinate variables to the MNC output from the diagnostics package
484    o change MNC-flags default value: true when useMNC=TRUE
485    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
486      the ability (off by default) to read the grid information using MNC
487    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
488    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
489    o do snap-shot diagnostics at the middle of the time-interval (instead of
490      at the end).
491    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
492      new test for AIM with thSIce + slab-ocean
493    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
494    o move state variable diagnostics to the beginning of the time step ;
495      (note: still needs some work specially for snap-shot diagnostics)
496      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
497    
498    checkpoint57c_post
499    o Change testing option (-ieee) to get closer agreement between g77 & ifort
500    o generate new output.txt files on faulks with g77 & the new -ieee option
501    checkpoint57c_pre
502    
503    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
504      update output.txt of exp. global_ocean.90x40x15
505    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
506      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
507    o add saltFlux(+File) forcing capability with periodicExternalForcing
508    o allow to use pkg diagnostics for GM-Redi & ThSIce output
509    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
510    o improvements for the MNC output from DIAGNOSTICS:
511      - correct handling of the unlimitied dimension
512      - all dims now have associated coordinate variables
513      - variables located at U, V, and Corner ("Z") points are now written
514        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
515        *all* data points are output
516    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
517    o added pkg/seaice/seaice_monitor.F
518    o mdsio_readfield.F can now read files visible only to master MPI process.
519    o pkg/seaice: some test code for ice-modified ocean stress
520    o exf_getffields interpolation defaults to bilinear for all scalar forcing
521      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
522      spurious negative numbers for precipitation and humidity.  Will cause
523      some small numerical differences for integrations using pkg/exf/exf_interp.F.
524    o pkg/ctrl/
525      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
526        May be enabled via doPackDiag
527      *  introduce z-scaling of
528         + gradient (doZscalePack) and
529         + control (doZscaleUnpack)
530    o pkg/mdsio/
531      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
532      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
533    
534    checkpoint57b_post
535    o simplify options in diagnostics_fill arguments (remove weird combinations)
536    o fix MNC coordinate variables so that they now contain per-face index
537      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
538      general, EXCH2 grids are only aligned to a "local" coordinate system
539    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
540    o Implement instantaneous output within pkg diagnostics:
541      setting a negative frequency in data.diagnostics produces
542     "snap-shot" output (as opposed to time-average if freq > 0)
543    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
544      NOTE: change ptracer diagnostics name: use 2 characters to work with
545            more than 9 tracers. Add also diagnostics of advect & diffus flux.
546    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
547      becomes the coordinate variable for the 'T' dimension
548    o add CF-style coordinate variables to MNC
549      - just a first cut:  numbers are meaningless on the cubesphere and
550        missing along the T axis but otherwise it works!
551    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
552    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
553    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
554      this is based directly on what the model compute, so that the content of
555      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
556    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
557    o clean up build options files for SunOS, in particular
558      - remove -traditional from xmakedepend
559      - change -xarch=v9 to -xarch=native for f77
560      - restore use of make (not gmake)
561      - add CC=gcc if using g77
562    o changes per discussion of AM, JMC, & EH3 today:
563      - move redundant "grid" variables out of "state" -- in preparation of
564        creating proper CF-style coordinate variables and in recognition
565        that any/all grid variables can be easily copied (eg. w/NCO) from
566        the grid files into any of the other NetCDF files
567      - *always* output grid variables with MDSIO (this will eventually be
568        changed)
569      - output MNC grid file if useMNC is true
570    o every instance of _END_MASTER() has been found and replaced with
571      _END_MASTER( myThid ) in order to satisfy certain picky Sun
572      preprocessors
573    o re-arrange diagnostics pkg initialisation:
574     - allow each package to extend the available diagnostics list
575     - add some checking and fix small problems (multi-threaded, ...)
576     - new S/R diagnostics_fill (replace fill_diagnostics):
577       look through the short list of active diag. (instead of the long list)
578       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
579    
580    checkpoint57a_post
581    o this set of changes restores TAMC compatibility
582      tested for global_ocean.90x40x15 adjoint on trough
583      (what a pain)
584    
585    checkpoint57a_pre
586    o some modifs in tools/build_options for sunos
587    o call ctrl_pack for ctrl at end for optimcycle=0
588    
589    checkpoint57
590    o add horizontal bi-harmonic viscosity for vertical velocity
591      - new parameter viscA4W (defaults to viscA4)
592      - affects only non-hydrostatic code
593      - to be done: no-slip lateral boundary conditions
594    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
595    o implement Implicit Vertical advection for pTracers
596    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
597      (implemented also for implicit vertical diffusion & advection)
598    o OBCS: extend application of tracer open boundary conditions
599      to a strip beyond the boundary of width Olx/Oly
600    o add call monitor to TAF set of required calls (flow directives)
601      and include in natl_box_adjoint
602    o untangle a few ifdefs related to cost, ctrl, autodiff
603      untangel a few ALLOW_ECCO_OPTIMIZATION
604    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
605      (theta2, salt2 in ecco_cost_weights)
606    
607    checkpoint56c_post
608    o OBCS as control variables
609      - update ctrl_ad_diff.list, obcs_ad_diff.list
610      - remove balance of obcs controls from default
611      - fix index bug nobcs in ctrl_init
612      - fix dummy fields filen in ctrl_pack
613      - add dummy weights for obcs
614    o lsopt: comment out fort.94 output
615    o optim:
616      - remove unnecessary header files
617      - adjusted namelists
618      - add xerbla.F to Makefile
619    o exf:
620      - multiple modifications of exf_check_range
621      - unit change in exf_init_runoff from [m/year] to [m/s]
622    o mdsio:
623      - i/o-vector change debugLevel from debLevA to debLevB
624    
625    checkpoint56b_post
626    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
627      is called from DO_THE_MODEL_IO
628      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
629      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
630      - clean up PTRACERS_WRITE_TIMEAVE a little
631    o add another verification experiment that tests both the cfc-pkg and
632      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
633      reactive tendencies treated inline with regular timestepping
634    o testreport previously did a lousy job of comparing small numbers, so
635      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
636      implemented in the little c-progam tmp_cmpnum.c which is embedded in
637      testreport.
638    o ptracers_monitor: bug fix for MPI
639    
640    checkpoint56a_post
641    o GCHEM: finish reorganizating the package
642      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
643        (introduces another 3D-array for each passive tracer, but only if
644        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
645        gchemTendency is not needed because the timestep is done separately)
646      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
647      - GCHEM is now---more or less cleanly---separate from PTRACERS
648      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
649        so clear to me how that should be done in a general way.
650    o CFC: improve formatting of output in CFC_ATMOS
651    o PTRACERS:
652      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
653        that ALL experiments with ptracers enable can be checked. This makes
654        GCHEM_MONITOR obsolete.
655      - include a runtime parameter PTRACERS_monitorFreq that defaults to
656        monitorFreq
657      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
658    o add PTRACERS (PTR0[1-5]) to testreport output
659    o exf_check_range:
660      * default changed to .TRUE.
661      * will check values for niter0 if debLevA, every timestep if debLevB
662      * STOP in exf_check_range if 'out of range'
663      * range chosen generous to allow for potential extema
664      TBD: a version with stricter range
665           permitted range would be runtime parameters
666  o GMredi:  o GMredi:
667    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;    - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
668    - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.    - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
# Line 11  o GCHEM: Line 671  o GCHEM:
671    - move call to GCHEM_FORCING_SEP, so that it is now called before    - move call to GCHEM_FORCING_SEP, so that it is now called before
672      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP      the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
673    - introduced a useGCHEM runtime flag and applied it everywhere.    - introduced a useGCHEM runtime flag and applied it everywhere.
674      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
675        this flag is now only visible within GCHEM-pkg routines.
676      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
677        be replaced by a 3D array that is computed before thermodynamics; for
678        this, the tracer ID iTracer had to be included into the parameter list
679        of ptracers_forcing
680      - set up forward_step to call gchem_forcing, that will replace
681        gchem_forcing_int in ptracers_forcing
682      - cleaning up
683  o small cleaning of exch2: remove files that are also in eesupp/src  o small cleaning of exch2: remove files that are also in eesupp/src
684    
685  checkpoint56  checkpoint56

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