/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.297 by mlosch, Wed May 19 08:43:38 2004 UTC revision 1.1912 by jmc, Wed Aug 14 21:16:35 2013 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    o pkg/diagnostics:
8      - add a parameter to track the status of pkg/diagnostics activation;
9        this replace/extend the use of logical param "settingDiags" (to check
10        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
11        New S/R to print error message and stop when pkgStatus is not right.
12      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
13    
14    checkpoint64m (2013/08/13)
15    o model/inc:
16      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
17        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
18    o pkg/kpp & aim_v23:
19      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
20    o pkg/seaice:
21      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
22        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
23      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
24    o eesupp/src:
25      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
26        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
27    o switch to TAF version-2:
28      - add flow directives to "freeze" naming convention for ad-routines that
29        are used in I/O routines of adjoint state and associated common blocks
30        that are used in adcommon.h (backward compatible with version-1)
31      - update all ad-optfiles (in tools/adjoint_options + few local to some
32        verification exp) to switch to latest TAF version (currently 2.5.5);
33        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
34        out except for diva).
35      - the major change with TAF version-2 is that both the differentiated
36        routines and the forward routines (new) are returned as part of the TAF
37        output source code. Update genmake2 accordingly.
38      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
39        with version-2 when compared to TLM or FWD gradient); other experiments
40        output show minor changes (machine truncation level); update the few AD &
41        TLM output with 12 matching digits only (some prior to version-2 switch).
42    
43    checkpoint64l (2013/08/05)
44    o model/src:
45      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
46      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
47        when using TAF but only if using OpenAD.
48    o pkg/mom_common+fluxform+vecinv:
49      - always set horiz. viscosity arrays to background value before calling
50        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
51        only when using variable horiz. viscosity (useVariableVisc=T);
52      - simplify mom_vecinv.F (only 1 block for momViscosity).
53    o pkg/mom_common: variable horiz. viscosity in NH code
54      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
55        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
56      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
57        useBiharmonicVisc & useVariableVisc.
58      - fix old bug (already in 1rst implementation of variable horizontal viscosity
59        in calc_gw.F, version 1.27, 2006/06/20):
60        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
61        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
62      - change background horiz viscosity in vertical momentum (gW) to always be
63        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
64        any type of variable viscosity, e.g., viscAh/4Grid)
65      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
66        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
67        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
68        default viscAh,viscA4 is zero).
69    o model/src:
70      - extend length of drC & recip_drC from Nr to Nr+1.
71    o Divided Adjoint (DIVA) with MPI:
72      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
73      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
74        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
75    
76    checkpoint64k (2013/07/23)
77    o tools/OAD_support:
78      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
79        and remove it from genmake2.
80    o tools/build_options:
81      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
82        MPI_HEADER_FILES list (let genmake2 find the missing headers)
83    o verification/halfpipe_streamice:
84      - change to driving stress formulation; update both Fwd & AD output.
85    o tools/genmake2 and Divided Adjoint with MPI:
86      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
87      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
88      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
89        Makefile, which is set by genmake2, and check which mpi-headers are needed.
90        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
91      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
92    o testreport:
93      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
94        perform additional runs (number of additional runs is "add_DIVA_runs" taken
95        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
96    o verification/lab_sea (AD test):
97      - change to test Divided Adjoint Run in this set-up (both standard AD test
98        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
99    o pkg atm_ & ocn_compon_interf:
100      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
101        staggerTimeStep implementation) and disable (retired) corresponding
102        parameter.
103    o pkg/offline:
104      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
105      - add S/R OFFLINE_CHECK to print offline parameter summary
106        and stop if loading a file that is not used;
107      - enable to calculate GMRedi tensor, KPP mixing and convective index
108        when the corresponding file(s) is/are not specified (but pkg is used).
109      - comment out resetting of monitorFreq (to endTime) since it still useful
110        for monitoring CFL numbers and checking offline fields.
111    o OpenAD:
112      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
113        smaller standard output) and generate new (smaller) output (on baudelaire
114        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
115    o model/src:
116      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
117        (where external_forcing_adjust was called) and change list of arguments;
118      - merge external_forcing_adjust.F into external_forcing_surf.F
119      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
120        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
121        previously in file "balance_relax.F", now removed); remove corresponding
122        arrays in FFIELDS.h.
123      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
124        a hack for getting back surfaceForcingS (loaded from file) when using
125        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
126      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
127        (was getting only 11 digits for AD-grad, due to different truncation
128         error in AD code).
129    
130    checkpoint64j (2013/07/04)
131    o pkg/offline:
132      - to enable the use of other features with pkg offline (e.g., obcs),
133        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
134      - comment out "allowFreezing" (now active) in 2 offline testing exp.
135    o pkg/exf ALLOW_RUNOFTEMP
136      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
137      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
138      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
139    o pkg/atm_phys:
140      - allows to add some damping on uVel,vVel (strength only function of k).
141    o verification, ad-tests:
142      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
143        global_ocean_ebm and offline_exf_seaice.thsice.
144    o verification/halfpipe_streamice:
145      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
146        flux input boundary conditions to be ignored; a fix for this bug changed
147        verification results for forward test.
148      - add adjoint test.
149    o pkg/ptracers:
150      - allow to restart without SOM pickup (resetting SOM to zero).
151    o pkg/gmredi:
152      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
153      - It uses mixing length theory and suppression by steering level effects to
154        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
155        to JPO, for more details).
156      - It also uses the diffusivity to calculate an eddy induced streamfunction
157        based on a PV closure (rather than a buoyancy closure as in GM).
158      - New files added to pkg/gmredi:
159        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
160          induced overturning streamfunction (called from gmredi_calc_tensor)
161        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
162          for use in gmredi_k3d
163        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
164          the eddy diffusivity
165    
166    checkpoint64i (2013/06/18)
167    o pkg/cheapaml:
168      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
169        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
170        with pkg/cheapaml.
171    o utils/python: add subpackage for cubed sphere function, first example is
172        simple cs.pcol to plot 2D fields on a map
173    o pkg/streamice:
174      - This is a new package in MITgcm, which solves dynamic equations for ice
175         sheets and ice streams
176      - At the moment it is independent of atmosphere/ocean dynamics, or any
177        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
178        ed that this will change)
179      - There is a new verification exercise that tests it, halfpipe_streamice,
180        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
181        rectangular embayment
182      - halfpipe_streamice is forward-only for now, will have TAF test soon
183      - for questions, email dgoldber@mit.edu
184    o pkg/thsice:
185      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
186        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
187      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
188         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
189      - allow precip from pkg/cheapaml to make snow over seaice.
190    o pkg/cfc:
191      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
192      - remove atmos CFC 2-D arrays from common bloc (now local variables)
193      - change some hard-coded constant to run time parameter for reading and
194        and interpolating atmospheric CFC ; keep same default as previously.
195      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
196      - put arguments in standard order: myTime, myIter, myThid
197      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
198        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
199      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
200      - new routine to print summary of CFC params and check for consistency.
201    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
202      similar to thsice_advdiff.
203      Note that for the B-grid case the routine parameters uc/vc are overwritten.
204    o pkg/cfc:
205      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
206        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
207      - fix interpolation of atmphspheric CFC between Sorthern and Northern
208        hemisphere value.
209    o pkg/seaice:
210      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
211    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
212                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
213      - requires an additional time level that is stored in the pickup
214      - you can start with AB2 from a pickup without this time level with
215        pickupStrictlyMatch = .false.
216    
217    checkpoint64h (2013/05/26)
218    o pkg/cheapaml:
219      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
220        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
221      - consistent treatment of uWind,vWind location: assume everywhere in
222        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
223        (Note: was already the case for Tair,Qair advection);
224        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
225      - compute diabatic forcing only in the interior (excluding overlap regions)
226      - fill in array "Qsw" (for short-wave heating);
227      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
228        before any update (consistent with MITgcm state var diagnostics);
229      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
230        non periodic ; + adjusted for uWind,vWind (C-grid).
231    o pkg/seaice:
232      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
233        add explicitly pkg/exf in experiments that currently use pkg/seaice.
234      - allows to compile pkg/seaice without pkg/exf.
235    o tools/OAD_support:
236      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
237        of array "ourStepOf" in function rvNextAction (revolve.F90).
238    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
239      - change pkg name (to be used with other atmospheric physics pkg)
240        but by-pass CVS when making the new pkg so that we keep the CVS history.
241    o pkg/offline:
242      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
243        (previously called from pkg/dic_surfforcing_init.F)
244    o model/src:
245      - re-order sequence of calls within packages_init_variables.F, using
246        standard order, except for:
247         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
248         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
249    o new pkg: atm_phys
250      - add entry point and source code (previously in contrib
251          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
252        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
253      - re-order sequence of calls within packages_readparms.F,
254         packages_init_fixed.F and packages_write_pickup.F
255        (but skip packages_init_variables.F because of TAF issues).
256      - update contrib/*/atm_gray/ experiment.
257    o pkg/seaice (ITD code):
258      - simplify and fix the writing of pickup-files for ITD case
259    o pkg/seaice (ITD code):
260      - introduce floe size dependent lateral melt for ITD case;
261      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
262      - update seaice_itd experiment main output.
263    o pkg/thsice:
264      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
265        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
266        changed accordingly pkg/atm2d.
267    
268    checkpoint64g (2013/05/01)
269    o pkg/exf ALLOW_RUNOFTEMP
270      - if defined,  river and glacier runoff temperature can be read-in from
271        runoftempfile; runoftempfile needs to have same format as runofffile
272    o pkg/thsice (& pkg/bulk_force):
273      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
274        for energy content of Precip + RunOff & Evap (like with pkg/exf).
275      - change computation domain to always be the interior (without overlap).
276      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
277    o verification/tutorial_global_oce_biogeo:
278      - add preliminary OpenAD setup (still has problems)
279    o pkg/seaice:
280      - turn some parameters for choosing the convergence criterion of
281        the inexact Newton method (JFNK) into runtime parameters for convenience
282      - clean up seaice_calc_viscosities.F: remove/retire two options for
283        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
284        the results of lab_sea/input because a division has been replaced by
285        a multiplication with the reciprocal (sumNorm)
286      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
287        convergence of solver (changes results, of course), and to test some
288        new features
289    o model/src:
290      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
291      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
292      - move forcing adjustment (balancing surface forcing) in specific S/R
293        where might also be applied exchanges (if needed) to forcing arrays.
294    o pkg/shelfice:
295      - allow to specify the Ice-Shelf mass per unit area (instead of
296        shelficeLoadAnomaly) and do the conversion from one to the other
297      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
298        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
299        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
300        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
301      - update isomip experiment forward output (get machine truncation error
302        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
303    o verification/offline_exf_seaice:
304      revise data.seaice in input.thermo and input_ad and update results accordingly
305        HO = 0.2, SEAICE_areaLossFormula = 2,
306        SEAICE_growMeltByConv = .TRUE.,
307        SEAICE_doOpenWaterMelt = .TRUE.,
308      Improve consistency with input.thsice and fix the spurious 500m ice corners
309    o verification/global_ocean.cs32x15:
310      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
311        in icedyn (thsice+seaice-dyn) test and update output.
312    o verification/offline_exf_seaice:
313      - adjust list of tested variables (with testreport) and update
314        standard test output with better slection of monitored fields.
315    o pkg/cd_code:
316      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
317        experiment lab_sea.hb87
318    o tools/genmake2:
319      - change default makedepend from the system default to tools/xmakedepend:
320        When no makedepend is specified, select tools/xmakedepend it the test pass,
321        otherwise select the system default (if exist and pass the test) or
322        try to build cyrus-makedepend ; stop if none of the 3 works.
323    o pkg/exf & pkg/thsice:
324      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
325        for energy content of Precip + RunOff & Evap. Assumes:
326       1) Rain has same temp as Air.
327       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
328       3) Run-Off comes at the temp of surface water (with same Cp)
329       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
330        put directly into Latent Heat flux & should use water-vapor heat capacity.
331       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
332        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
333    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
334        (compile when SEAICE_ALLOW_JFNK is defined)
335    o pkg/thsice:
336      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
337        implementation): move THSICE_AVE call after the advection (called directly
338        from thsice_do_advect.F).
339    o verification/global_ocean.90x40x15 and OpenAD:
340      New experiment for OpenAD is identical to the one in input_ad except that
341        multiDimAdvection=.FALSE.,
342      There is still an issue with this.
343    o pkg/thsice:
344      - account for ice velocity (ocean relative velocity) in turbulent heat flux
345        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
346        and offline_exf_seaice (main test).
347    
348    checkpoint64f (2013/03/31)
349    o verification/OpenAD:
350      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
351    o verification/isomip, pkg/shelfice and OpenAD:
352      - add OpenAD setup to this exp and make shelfice package work with OpenAD
353    o verification/tutorial_global_oce_biogeo:
354      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
355    o verification/offline_exf_seaice:
356      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
357    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
358      - add OpenAD setup to this exp and make ptracers package work with OpenAD
359    o pkg/seaice/seaice_evp.F:
360       mask the asymmetric contribution of the ice-ocean stress (when
361       the turningAngle is non-zero) over open water to avoid stripes
362       in the EVP-solutions after many EVP-substeps. This does not change
363       the verification experiment (because turningAngle=0 in that experiment),
364       but will affect other EVP solutions with turningAngle.ne.0
365    o verification, AD & TLM output:
366      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
367        additions and multiplications which affect results at machine truncation
368        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
369        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
370        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
371        digits of matching.
372    o pkg/seaice:
373       modify lsr-algorithm so that it vectorizes AND converges by using a
374       "zebra" method: split vector loop into two with step size 2; this
375       solves a general convergence problem for the JFNK solver on a vector
376       computer. It has the potential to even improve convergence for
377       non-vector machines, but it does change the results so it is turned
378       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
379       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
380    
381    checkpoint64e (2013/03/05)
382    o pkg/ecco and several verification experiments:
383       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
384       from ecco package, and revert to unified routine in model/src/
385       Adjust verification experiments accordingly, especially gloal_oce_llc90
386       Should conclude long-standing work by Gael to reconsile the_main_loop with
387       ECCO and will enable OpenAD's revolve loop in ECCO setup.
388    o pkg/generic_advdiff:
389      - implement compressible flow method for multi-dim advection (similar to
390        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
391        TAF generates many recomputations) to use it; no yet coded with implicit
392        vertical advection.
393      - change experiment advect_cs (new output) and advect_xy (same output)
394        to test compressible flow multi-dim advection.
395    o pkg/generic_advdiff:
396      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
397        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
398    o pkg/seaice:
399      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
400        bug affects two verification experiments (lab_sea and lab_sea.hb87),
401        recover old (wrong) results by setting noSlipFac = 2. in
402        seaice_calc_strainrates.F;
403      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
404      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
405        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
406      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
407    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
408      - new subroutines seaice_lsr_tridiagu/v
409      - introduce loop bounds i/jmin/max to be able to use a restricted
410        additive Schwarz method, but not used for now.
411      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
412      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
413    o OpenAD support
414       Reorganize S/R call for overall time-stepping loop to facilitate
415       OpenAD revolve loop replacement
416       (new S/R main_do_loop.F)
417    o model/src:
418      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
419      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
420        ADAMS_BASHFORTH2.
421    o pkg/cheapaml:
422      - add new parameter (default=F, same as before) to disable full domain
423        (including land) periodicity in X & Y dir.
424      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
425        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
426        into single S/R CHEAPAML_TIMESTEP.
427    
428    checkpoint64d (2013/02/17)
429    o pkg/monitor (angular momentum):
430      - do not add Eta contribution to the total AM if using rigid-lid;
431      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
432      - horizontal discretisation: compute Zonal wind contribution separately for
433        each component (instead of from cell centered averaged) and use the 4
434        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
435      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
436        FreeSurf) if using vectorInvariant momentum.
437    o model/src (horizontal grid):
438      - move initialisation of all horizontal grid arrays to null value
439        from specific horizontal grid S/R to main S/R INI_GRID;
440      - add 2 new arrays to project model C-grid velocity on to zonal direction
441        (similar to AngleCosC & -AngleSinC but at U and V point location) and
442        compute them in S/R CALC_GRID_ANGLES.
443    o pkg/seaice: replace a hard coded parameter by a runtime parameter
444        SEAICE_JFNK_tolIter
445    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
446        preconditioner for JFNK (run LSR into the overlaps as far as possible,
447        i.e OLx/y-2, but overwrite the solution in the overlaps)
448      - extend loop range in seaice_calc_viscosity
449      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
450      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
451      - slightly modify loops in tridiagonal solver lsr-preconditioner
452      - by default remove the extra exchange in seaice_preconditioner with a
453        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
454      - modify offline_exf_seaice so that old results without RAS are reproduced
455        for output.dyn_jfnk.txt
456      in seaice_fgmres.F (unrelated to RAS)
457      - add a cpp-flag option for a re-ordered mapping (potentially more
458        efficient), but because this changes the results, turn it off by
459        default
460      - replace the save statement by local common blocks
461    o utils/matlab:
462      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
463      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
464        instead of local script "load_cs.m".
465    o pkg/seaice:
466      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
467        to the scalarProductMetric and the unrolling. By chance this does not
468        change the verification experiment, because of the particular domain
469        decomposition
470    o pkg/diagnostics:
471      - change default missing_value from UNSET_RL to -999.
472    o pkg/layers: improve vectorization of layers_fluxcalc.F
473      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
474        time spent in this routine by more than a factor of 3 on an NEC-SX8
475      - step 2: replace search algorithm by a bisection algorithm found in
476        Press et al. Numerical Recipes in Fortran. This algorithm can be
477        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
478        For now, use this algorithm only for TARGET_NEC_SX defined.
479      - moved the search algorithm into a separate subroutine, that is kept
480        within the same file for automatic inlining.
481      - modified catching potential errors
482    o pkg/ecco:
483      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
484    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
485      - modifications for ALLOW_GENTIM2D_CONTROL
486      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
487      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
488      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
489      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
490    o model/src:
491      - account for moist thermodynamics in (dry) potential temperature equation;
492        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
493        and cpl_aim+ocn.
494      - also switch to standard compiler (gfortran, was using ifort previously)
495        for fizhi-cs experiments reference output.
496    o pkg/ctrl:
497      - 1st step toward generic time-varying control variable (2D) via CPP option
498        ALLOW_GENTIM2D_CONTROL
499      - note new namelist ctrl_nml_genarr in data.ctrl
500    o verification/global_ocean.cs32x15:
501      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
502        thsice calling sequence and update "output.icedyn.txt" output file.
503    o pkg/ptracers:
504      - from Ryan A.: code to allow to restart a tracer at regular time interval
505        specifying a reset frequency and a reset-phase (for each tracers).
506    o pkg/thsice:
507      - implement new sequence of calls for thsice+seaice:
508          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
509          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
510      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
511        in CPP_OPTIONS.h) to recover old sequence;
512      - update diagnostics for Intermediate State thsice diagnostics: now filled
513        just before advection (instead of just after advection in old sequence);
514      - update output of experiment offline_exf_seaice (standard test);
515      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
516        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
517    o pkg/aim_v23:
518      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
519      - use standard pkg/mdsio routines to read & write CO2 pickup file;
520      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
521      - Implement new sequence of calls for seaice advection (with thsice and
522        seaice diffusion): do ice advection after ice-Thermodynamic (previously
523        was done before); change aim_do_physics.F (split the bi,bj loops block);
524      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
525    o pkg/thsice:
526      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
527        where just seaice diffusion is used without seaice-dynamics.
528    
529    checkpoint64c (2013/01/18)
530    o pkg/seaice:
531      - add a parameter JFNKres_tFac that can replace JFNKres_t
532        (= JFNKres_tFac*JFNKresidual before JFNK solver)
533      - add a line search option to the JFNK solver
534      - move update of u/vIce and computation of initial residual into a separate
535        routine (same file); makes the code a little easier to read (?)
536      - the line search requires computation of the residual and for some reason
537        I cannot do the update of u/vIce at the beginning of the Newton loop
538        without changing the results, so we move computation of the new residual
539        also to the end of the Newton loop, even without the line search
540    o pkg/mdsio:
541      - write missing value (corresponding to undefined array value) to meta files;
542        skip this if missing value is one (UNSET_RL would be a better value for the
543        case of undefined missing value but it's current the default missing-value);
544        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
545    o pkg/exf & thsice:
546      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
547        diagnostics) even when SHORTWAVE_HEATING is #undef;
548    o verification/cfc_example:
549      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
550        illustrate how to use it).
551    o verification/offline_exf_seaice:
552      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
553        files to only one time-record.
554      in input.thermo: narrow the 2 bands of low initial ice-concentration near
555        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
556        snapshot output; same mcPheePiston value as in thsice with
557        surf-current=0.2m/s.
558      in input.thsice: similar set-up as in input.thermo (channel with same seaice
559        initial conditions).
560    o verification/cfc_example:
561      - update file "data" with more standard choice (default rotationPeriod,
562        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
563        set deltaTFreeSurf to deltaTtracer) and update the output.
564    o pkg/layers:
565      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
566      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
567    o verification/offline_exf_seaice:
568      - set all {field}period to zero for constant-in-time forcing (not tested
569        anywhere else).
570    o verification/offline_exf_seaice:
571      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
572      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
573    o model/src:
574      - implement Finite-Volume method for (hydrostatic) presure gradient
575        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
576    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
577      - In order to be compatible with the default EVP code, this requires changing
578        the EVP code around a little; and because any small change immediately
579        breaks the lab_sea.hb87 verification experiment, the reference output is
580        updated two times (each time the remaining aggrement was only 2 digits):
581        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
582        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
583        The adjoint test lab_sea.evp also needed to be updated.
584      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
585        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
586        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
587        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
588        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
589        kept obscure, because I need to test it a little more.
590    o pkg/cheapaml:
591      - fix few incorrect type (_RL/_RS) in subroutine calls.
592    o pkg/seaice:
593      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
594        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
595    o model/src:
596      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
597        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
598        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
599    o pkg/cheapaml:
600      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
601        update output of experiment cheapAML_box.
602      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
603        and set them only in one place (cheapaml_readparms.F).
604      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
605      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
606        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
607    o model/src/the_main_loop.F:
608      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
609    o pkg/seaice:
610      - remove legacy branch code.
611      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
612    o verification/*/code*/SEAICE_OPTIONS.h:
613      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
614        SEAICE_CAP_HEFF).
615    o pkg/cheapaml:
616      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
617        to load new forcing fields.
618      - add missing "_d 0" where it's needed; + some editing (improve indentation).
619      - remove switch to "-r8" compiler option (no longer needed) in verification
620        cheapAML_box, keep same output (small trucation error differences).
621    o verification/offline_exf_seaice:
622      - add thermodynamics only test.
623    o verification/cheapAML_box:
624      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
625        keep same output (same 14 digits for cg2d).
626      - switch on "-r8" compiler option (some numerical values are missing
627        the "_d 0") and update output (only 6 digits for cg2d were preserved).
628    
629    checkpoint64b (2012/12/24)
630    o pkg/cheapaml:
631      - remove un-used variables (Qnet,EmPmR) from pickup files.
632      - store tendency of advected variables into cheapaml pickup file
633        and fix the AB-2 restart.
634    o verification/offline_exf_seaice and lab_sea adjoint:
635      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
636      - switch to 4 time steps in offline, consistent with lab_sea.
637      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
638      - update results after change of experiment seaice.
639    o pkg/seaice:
640      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
641        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
642        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
643        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
644    o model/src:
645      - add run-time parameter to select CG2D solver minimum-residual solution
646        (in case of a poor convergence).
647    o pkg/seaice/seaice_lsr.F
648      - move calculation of matrix coefficients into new
649        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
650        file; the main purpose of this change is to be able to reuse the code
651        in S/R SEAICE_PRECONDITIONER
652      - modify the computation of the residual so that the mass of sea-ice
653        is not used twice; this simplifies the calculations, but since
654        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
655        not tested in testreport---this does not affect the testreport results.
656    o verification/seaice_obcs:
657      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
658        verification/lab_sea/input.salt_plume; changes results/output.txt*
659    o model/src:
660      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
661    o pkg/seaice:
662      - improve description of parameters in seaice_fgmres.F and start
663        cleaning up the code
664      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
665        second argument
666      - add a metric based on grid cell area to SEAICE_SCALPROD; update
667        results of offline_exf_seaice.dyn_jfnk
668      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
669    o pkg/aim_v23:
670      - fix an other bug in dissipation heating (grid-cell area was missing).
671    o model/src + pkg/seaice:
672      - add global (multi-tile) linear solver for pair of tri-diagonal system
673        along X and Y lines, respectively for U and V component.
674        Note: 1) MPI and cube-exchange not yet coded.
675            2) probably not accurate for poorly conditioned / large size problem.
676      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
677        default: not compiled and not used.
678    o pkg/seaice:
679      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
680        introduce bi/bj loops and use global_sum_tile_rl instead of
681        mpi_allreduce in seaice_fgmres.F
682      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
683      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
684      - add a verification experiment for JFNK in offline_exf_seaice
685    o verification:
686      - change (for now, only fwd test) offline_exf_seaice experiment:
687        use a re-entrant channel with idealized coastline (trapezoidal shape)
688        at southern boundary to explore seaice dynamics and thermodynamics
689        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
690        secondary test (input.thsice) use thermodynamics only with SST relaxation.
691      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
692    o pkg/exf:
693      - disable "sstExtrapol" when Nr=1
694    o verification:
695      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
696        to test pkg/cheapaml.
697    o pkg/aim_v23 & pkg/shap_filt:
698      - fix dissipation heating (erroneous gravity multiplication factor).
699    o pkg/seaice:
700      - remove unused field pressPre from jfnk solver
701      - rename two subroutines in seaice_preconditioner.F
702    o eesupp/src:
703       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
704    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
705       - remove wrong parts of the rhs and the lhs (were in there
706         because I did not understand the concept of this preconditioner)
707       - add an exchange between u- and v-sweep. This increases communication
708         by a factor of two but improves the convergence of jfnk. Ideally,
709         one would like the u- and v-sweep to be independent. So far within
710         undocumented ifdefs
711       - reorganize the extra computations for printing the residuals
712    o tools/genmake2:
713      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
714        since it's not necessary (and was preventing to use MNC in some cases).
715    
716    checkpoint64a (2012/11/16)
717    o pkg/autodiff:
718      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
719        autodiff_readparms.F no longer depends on calling order (within
720        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
721        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
722        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
723    o pkg/obcs:
724      - adding tidal velocity forcing capability to obcs
725        for usage example, see verification/seaice_obcs/input.tides
726    o pkg/seaice:
727      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
728        SEAICE_LSRrelaxU/V
729      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
730    o pkg/aim_v23:
731      - implement heating from friction (bottom friction and stratospheric drag).
732    o pkg/shap_filt:
733      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
734        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
735    o model/src:
736      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
737        time-constant addMass field from file (addMassFile);
738      - support for heating due to friction (and Kinetic Energy dissipation):
739        add option, run-time switch and 3-D field array + support code ; each pkg
740        or S/R can add heating contribution (if there is a sink of KE); the sum is
741        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
742    o pkg/seaice:
743      - complete merge of ITD code into seaice_growth.F
744        from MITgcm_contrib/torge/itd/code/
745        no verification so far, but Torge Martin tested
746        "1-D test case and Beaufort set up;
747        deliver okay results after 1 model year."
748      - complete merge of SEAICE_SIZE.h into all relevant routines
749      - move computation of eta at Z-points into calc_viscosities
750        + introduce global field etaZ
751        + add different methods for computing etaZ, for now the old
752          method (simple averages of eta to Z-points) is hardwired
753        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
754          seaice_preconditioner
755      - simplify computations for SEAICE_ZETA_SMOOTHREG
756      - seaice_preconditioner:
757        + replace one remaining press by pressLoc (mistake)
758        + adjust printing of residuals
759      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
760        + add (SEAICE.h) and rename some counters (initiliased in
761          seaice_init_fixed.F)
762        + add _BEGIN/END_MASTER (myThid)  around print statements
763        + print total number of iterations and failures over SEAICE_monFreq
764          interval to STDOUT
765      - move control over output-messages by fgmres to seaice_jfnk to save
766        some operations
767      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
768        in order to make restarts with sol .ne. zero (fgmres with restarts)
769        (seaice_jfnk.F, seaice_fgmres.F)
770      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
771        a serious convergence problem when open boundaries are involved
772    o pkg/ggl90: fix computation of control volumes for the case of
773      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
774      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
775    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
776    o pkg/autodiff
777      - Add inAdMode switch for SEAICEuseDYNAMICS:
778        SEAICEuseDYNAMICSinAdMode
779        (extend logic in ADAUTODIFF_INADMODE_SET)
780    o pkg/seaice
781      - Step 1 of merging ice-thickness distribution (ITD) code from
782        MITgcm_contrib/torge/itd/ (author: Torge Martin)
783        The code implements concept laid out in Thorndike et al. (1975);
784        code is enabled via CPP flag SEAICE_ITD
785        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
786        code is not complete yet!!
787      - SEAICE_SIZE.h now included in almost all seaice routines
788    o verification (using seaice):
789      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
790        global_ocean.cs32x15.seaice ; update results.
791      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
792      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
793        offline_exf_seaice (previously compiling B-grid).
794    o pkg/exf:
795      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
796        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
797        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
798    o pkg/layers (adjust changes from Sept 19):
799      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
800        this allows to remove "layers_maxNum" dimension from all layers arrays.
801    o pkg/layers (adjust changes from Sept 19):
802      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
803      - snap-shot extended to all type of layers (not just the 1rst type);
804      - remove layers variables when corresponding CPP option is undef.
805    o pkg/layers:
806      - rename pkg/layers variable and add new output (layer exist & un-weighted
807        velocity in layer)
808    o pkg/seaice:
809      - simplify (?) ocean-drag coefficent computations by using
810        the same routine in all three solvers (saves some code lines)
811      - remove global fields DRAGA and DRAGS from C-grid code and
812        declare them locally in lsr.F (the only place where they are
813        still used)
814      - update AD output of lab_sea.evp (very sensitive anyway).
815    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
816      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
817      and SEAICEuseJFNK=.true. A few things to note:
818      - involves a FGMRES, that is parallel but very inefficient,
819        because of many scalar products (global sums) in the Gram-Schmidt
820        orthogonalization method. Needs to be replaced. Original code
821        from J.-F. Lemieux
822      - preconditioner for FGMRES is a stripped down version of LSOR
823      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
824        preconditioner. For the preconditioner, the default is set to 10.
825      - Jacobian times vector is computed with finite differences
826      - marginally related to JFNK-solver: add a smooth regularization for
827        zeta with tanh that will improve convergence (Lemieux and Tremblay,
828        2009) for any implicit solver (not implemented for EVP because EVP
829        does not need this regularization in the first place). Define
830        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
831    o eesupp/src:
832      - check in genmake2 that intrinsic S/R flush is available.
833      - add S/R to flush IO unit (if intrinsic S/R flush is available)
834      - flush standard & error msg unit before MPI termination
835      - if debugMode, flush IO unit after printing msg
836    o pkg/ctrl:
837      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
838        to ctrl_set_unpack_xyz.
839    
840    checkpoint64 (2012/10/09)
841    o pkg/shelfice
842      - in mom_fluxform.F, mom_vecinv.F:
843        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
844        Bug fix KappaRU -> KappaRV
845        does not change verification/isomip but may change other setups
846        (presumably constant KappaRU=KappaRV)
847      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
848    o pkg/obcs:
849      - fixed some indexing bugs in obcs_seaice_sponge.F
850      - added obcs relaxation subroutines for HSALT and HSNOW
851      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
852    o pkg/seaice:
853      - add "multicategory" parameterization for snow in analogy to ice,
854        default is off for now.
855    o pkg/obcs:
856      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
857        see verification/seaice_obcs/input.seaiceSponge for example application.
858      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
859        index setting by master-thread. This fix multi-threads Pb in previous modifs.
860    o pkg/layers :
861      - add diagnostics to pkg/layers
862      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
863        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
864    o pkg/generic_advdiff/gad_implicit_r.F :
865      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
866    o pkg/seaice/seaice_growth.F:
867      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
868    o pkg/obcs:
869      - change default setting of OBCS_UVICE_OLD from defined to undef;
870      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
871        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
872      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
873      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
874        with Southern & Western OB at a tile edge (at least in a simple set-up).
875    o pkg/obcs:
876      - change settings of OB index in case OB coincides with tile edge (shared by
877        2 tiles), so that common OB location is registered by both tiles (instead of
878        only 1). However, for Southern and Western OB, index value = 0 is not
879        recognized as valid OB index (=default null value) and needs to be fixed.
880      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
881      - new parameter "OB_indexNone" for null index value (for now, still zero)
882        to replace hard-coded null index value of zero.
883    o pkg/exch2:
884      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
885        always check buffer-size (but outside the loop); move checking for valid
886        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
887        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
888    o pkg/ctrl (pack & unpack):
889      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
890        (locally defined) for different variables (+ remove the variable-specific
891        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
892        (to be extended to other local file names in ctrl.h).
893    o pkg/flt:
894      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
895    o pkg/mdsio:
896      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
897    o tools/genmake2:
898      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
899        (added by Alistair in version 1.51 for building without make depend);
900      - remove Header files list (H_SRC_FILES) from the dependence of targets
901         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
902        place in version 1.23): this save going through staf when unrelated header
903        file has been modified.
904       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
905        "make depend" step, still need to do "make links" before "make adtaf".
906    o eesupp/src (+ few pkg src files) & genmake2:
907      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
908      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
909      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
910         upper/lower case ; account for space between "#" and undef/define)
911    o pkg/flt (with exch2):
912      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
913      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
914    
915    checkpoint63s (2012/09/05)
916    o pkg/ecco:
917      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
918      - add more relevant #ifdef ALLOW_SMOOTH ones.
919      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
920    o pkg/ctrl:
921      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
922        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
923      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
924        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
925        ctrlSmoothCorrel3D (new).
926        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
927      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
928      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
929        controls when useAtmWind, and vice versa.
930      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
931      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
932          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
933      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
934          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
935      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
936        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
937    o pkg/smooth:
938      - remove un-necessary includes.
939      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
940        Those CPP options were never defined, and not necessary.
941    o model/src:
942      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
943      - standard treatment of useSMOOTH.
944    o pkg/autodiff:
945      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
946        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
947    o pkg/exch2:
948      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
949        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
950      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
951        and tiles to process mapping.
952      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
953        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
954        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
955        from w2_eeboot.F to w2_readparms.F.
956    o eesupp/src:
957      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
958        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
959        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
960      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
961        is defined (remove condition on usingMPI) to match cases where MPI_INIT
962        has been called.
963      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
964      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
965        (so that on 1 proc, get same myPid independently of usingMPI)
966      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
967        useCubedSphereExchange with EXCH-1 (safer).
968      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
969    o pkg/ggl90:
970      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
971        used in ALLOW_GGL90_SMOOTH code.
972    o pkg/flt:
973      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
974        floats at the Southern end of the domain).
975    o eesupp/inc:
976      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
977        but not used (and not to be used) anywhere, just for documentation.
978    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
979      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
980        a) can damage previously written records in any other multi-record files.
981        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
982    o tools/genmake2:
983      - define variable MAKE within Makefile and use it in place of 'make';
984      - update AD_CONFIG.h (if needed) before building any of the executable
985        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
986        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
987      - always print usual warning comment 'this file is automatically generated'
988        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
989    o pkg/cheapaml:
990      - updated to correspond to the code used in accepted paper (Nico Wienders).
991    o pkg/exf:
992        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
993        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
994        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
995    o pkg/exf, autodiff, ctrl, ecco and seaice:
996        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
997    o pkg/ctrl, ecco:
998        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
999        Depending on useAtmWind, one is inactive, and the other is active (see
1000        exf_getffields.F/exf_getsurfacefluxes.F).
1001    o tools/genmake2:
1002      - improve error msg when failing in 2nd test of check_for_broken_Ff
1003      - fix option '-makefile' short-name (-mf according to genmake2 -help)
1004      - source local config file "genmake_local" just after processing the genmake2
1005        command arguments (previously done before processing arg).
1006    o pkg/grdchk:
1007      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
1008        to this routine from cost_final has been dropped in g_cost_final)
1009      - improve printed information (more explicit msg, no longer using "print *,"
1010         fix fcpertminus printed value).
1011    o model/src:
1012      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
1013        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
1014        this prevents getting cost-funct reset in adinitialise_varia recomputations.
1015    o pkg/dic:
1016      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
1017        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
1018    o pkg/grdchk:
1019      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
1020      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
1021    o pkg/autodiff/ctrl/grdchk :
1022      - attempt to sort out what works and what does not,
1023        with regard to I/O, and to warn/stop accordingly.
1024    o pkg/grdchk:
1025      - attempt to fix grdchk in the case of useSingleCpuIO.
1026      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
1027       statements were moved from grdchk_main.F and into
1028       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
1029      - a global sum is applied to record numbers icvrec/layer
1030       out of grdchk_loc so that they be passed to I/O routines.
1031    o pkg/smooth:
1032      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
1033        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
1034    o verification/testreport:
1035      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
1036      - can also use compressed (gzip) reference output file;
1037      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
1038        to be easier to collect by testreport.
1039      - update existing TLM output (half out-of-date by more than 3 yrs).
1040      - report NETCDF & LAPACK settings (from genmake2) in output dir.
1041      - report run-time in each individual summary (previously only for AD test);
1042        for TLM test, add also TAF version.
1043      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
1044    
1045    checkpoint63r (2012/08/15)
1046    o tools/genmake2:
1047      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
1048    o pkg/ecco/ecco_cost_final.F :
1049      - fix fc print statements (to stdout and costfunction0000) so
1050        that the printed value is always after the global sum.
1051    o pkg/seaice/seaice_dynsolver.F :
1052      - fix ice strength assymptote at SEAICE_area_max<1
1053        (no change for the standard case of SEAICE_area_max=1)
1054    o some cleaning:
1055      - pkg source files: ensure that all *.F files from each pkg included the
1056        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
1057        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
1058        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
1059        includes;
1060      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
1061      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
1062        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
1063        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
1064      - update option-file CPP_OPTIONS.h of all AD experiments:
1065        * no longer include PACKAGES_CONFIG.h ;
1066        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
1067        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
1068          including ECCO_CPPOPTIONS.h).
1069    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
1070      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
1071        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
1072        not necessary accurate).
1073      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
1074        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
1075        deliberately break compilation (a remainder that it needs to be customized)
1076      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
1077      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
1078      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
1079    o tools/genamke2:
1080      - check for lapack.
1081    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
1082      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
1083        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
1084        from both packages.
1085      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
1086      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
1087      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
1088        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
1089    o pkg/cost : add comments to explain special and/or untested setups.
1090    o pkg/exf:
1091      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
1092        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
1093    o verification/*/code_ad:
1094      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
1095      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
1096      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
1097        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
1098    o pkg/seaice :
1099      - added possibility to change ice strength/PRESS0 relationship to
1100        HEFF, according to the following run time parameters
1101        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
1102        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
1103        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
1104    o pkg/ggl90 :
1105      - added run time flag mxlSurfFlag to include the code that ensure
1106        mixing between first and second level (previously included as a comment)
1107    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
1108      - add test of newly added dumpAdByRec=T option where
1109        we write all records to one file per variable.
1110    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
1111      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
1112        to check that this code is ok with taf and compiles in adjoint.
1113    o pkg/autodiff :
1114      - added run time param dumpAdByRec : ad dump format switch.
1115        If true then write all records to one file per variable.
1116        Else write one file per record (remains the default).
1117      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
1118    o pkg/seaice:
1119     - Added SEAICEuseTILT run time switch : if set to
1120       false then omit the tilt term in seaice dynamics.
1121     - Fix free drift calculation.
1122    o pkg/shelfice:
1123      When initializing SHELFICEDragQuadratic, set default to be
1124      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
1125      but retain option to set it independently
1126      (inconsistenty spotted by Veronique Dansereau)
1127    o eesupp/inc:
1128      - in EEPARAMS.h, add real-type constant for some frequently used simple number
1129         (0,1,2,1/2), with name explicitly referring to RS/RL type.
1130    o model/src:
1131      - move balancing of relaxation terms to new S/R balance_relax.F.
1132    o pkg/autodiff:
1133      re-write active I/O high-level (control) S/R:
1134      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
1135      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
1136      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
1137        MDS_READ/WRITE_FIELD); change loops to multi-threads.
1138      - update and merge active_file_control_slice.flow into active_file_control.flow
1139      - update the calls in lower level S/R (active_file.F, active_file_g.F and
1140        active_file_ad.F) keeping the argument list and function unchanged.
1141      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
1142        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
1143      - new low-level active I/O routines, one for each type (RL/RS), for active var
1144        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
1145        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
1146        right type.
1147    o autodiff and RS=real*4:
1148      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
1149        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
1150      - change argument type of 3-D mask argument to _RS to match type in the call
1151        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
1152    o pkg/thsice:
1153      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
1154      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
1155        fresh-water flux: uniform correction or proportional to local precip.
1156    o pkg/ctrl:
1157      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
1158      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
1159                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
1160      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
1161    
1162    checkpoint63q (2012/07/30)
1163    o pkg/autodiff:
1164      note about monitor and snap-shot of ad-variables:
1165      a) need to apply ADEXCH before monitor or output of ad-vars to include
1166       overlap contributions (was done for adjDump but missing for monitor).
1167      b) since ADEXCH implies adding overlap values to interior array, machine
1168       truncation error is expected when adding an ADEXCH call in the middle of
1169       the time-stepping (although mathematically identical).
1170      modifs:
1171      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
1172        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
1173      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
1174        apply ADEXCH before monitor or snap-shot of ad-variables:
1175           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
1176      - implement new method (copy+adexch) for snap-shot and monitor of main model
1177        ad-vars (initially not used by default -> output unchanged).
1178      - change default (set to 2) to use new method and update few output_adm.txt
1179        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
1180        and both tutorial_tracer_adjsens tests).
1181      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
1182        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
1183    o pkg/ctrl:
1184      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
1185      generic control variables via
1186      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
1187      Only required customization should be S/R ctrl_map_ini_genarr.F
1188      (routine in repository contains example)
1189    o pkg/exf:
1190      - fix and refine checking of surface-relaxation setting when using EXF
1191    o verification (adjoint exp):
1192      - reduce length of simulation by half for experiment global_ocean.cs32x15
1193        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
1194    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
1195      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
1196        of KE that can occur with aggressive optimization
1197      + put quadratic bottom drag calculation in separated loops (only done if
1198        using bottomDragQuadratic)
1199    o model/src: CG2D_NSA
1200      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
1201         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
1202      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
1203         change cg2d residual target to be expressed in Wunits (=> do not normalise
1204         RHS ; this fix global_max Pb with TAF); update output.
1205    o verification/tutorial_tracer_adjsens:
1206       improve parameter consistency (and get rid of warnings):
1207       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
1208       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
1209       - use staggerTimeStep (for stability) in som81; use default rotation period.
1210    o pkg/exch2:
1211      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
1212        reset to 0 = 1 long line in X)
1213    o pkg/mdsio:
1214      - fix reading of dimensions from meta file for large-size domain
1215    o model/src:
1216      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
1217      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
1218        Cubed-Sphere Exch with CS-corners inside the domain;
1219        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
1220        globalArea and to set hasWetCSCorners.
1221      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
1222        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
1223      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
1224        useCDscheme and useCubedSphereExchange).
1225    o pkg/seaice/seaice_growth.F :
1226      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
1227        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
1228        when the previous code was not correct.
1229      - in all cases diagnoze the boundary condition mismatch to SIaaflux
1230      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
1231        that term to QNET (essentially to set the melt/freeze water to 0degC).
1232        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
1233    o verification/global_ocean.cs32x15/input.seaice :
1234      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
1235      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
1236      - update results (output.seaice.txt) accordingly.
1237    o verification/lab_sea/input/data.seaice :
1238      - remove SEAICEheatConsFix, which is now be tested
1239        in global_ocean.cs32x15. The presently coded fix
1240        is only consistent with real fresh water + nlfs.
1241      - update results (output.txt) accordingly.
1242    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
1243    o AD_CONFIG.h file:
1244      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
1245      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
1246        add it explicitly in each fortran src file where it is needed.
1247        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
1248        thus introducing potentially wrong dependency; therefore, better to include
1249        it only where it's really needed, and after any other included OPTIONS file
1250        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
1251        or ALLOW_TANGENTLINEAR_RUN).
1252    
1253    checkpoint63p (2012/07/06)
1254    o pkg/autodiff:
1255      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
1256      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
1257        which are now read from new parameter file "data.autodiff" (inAdExact
1258        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
1259      - add file "data.autodiff" in all verification/*/input_ad/ directories.
1260      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
1261        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
1262    o verification/tutorial_tracer_adjsens/
1263      - add extra sub-verification which uses "SOM" advection scheme
1264        (2nd Order-Moment Advection Scheme, Prather Limiter) with
1265          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
1266        and in data:
1267          multiDimAdvection=.TRUE.,
1268          tempAdvScheme=81,
1269          saltAdvScheme=81,
1270    o model/src:
1271      - introduce ALLOW_BALANCE_RELAX which allow the removal
1272       of the global mean of relaxation terms by setting
1273       balanceThetaClimRelax and balanceSaltClimRelax
1274      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
1275       This case is now treated appropriately in seaice_growth.F
1276    o pkg/seaice:
1277      - do balanceEmPmR and balanceQnet based on the net fluxes
1278        (SItflux) that enter the ocean+ice system rather than QNET
1279        and EMPMR. Works best in real fresh water.
1280      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
1281        out of the diagnotics bloc, and stored in global arrays.
1282    
1283    checkpoint63o (2012/06/29)
1284    o vertical mixing schemes:
1285      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
1286      - replace computation of density (in Function STATE1, opps_calc.F) by a call
1287        to S/R FIND_RHO_SCALAR
1288      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
1289        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
1290        affects output (vermix.ggl90) at truncation level.
1291    o testreport:
1292      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
1293        (nSx,nSy) for the number of threads (from eedata.mth)
1294    o model/src:
1295      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
1296        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
1297    o verification/tutorial_tracer_adjsens/
1298      - compile with ALLOW_CG2D_NSA
1299      - run with nonlinFreeSurf=3
1300      - update reference output_adm.txt
1301    o tools/genmake2:
1302      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
1303        refine usePROFILES switching off (only when NetCDF is not available).
1304    o verification (atmospheric set-up):
1305      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
1306    o pkg/profiles : refine profiles and files handling.
1307    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
1308    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
1309      - changes to use model/src/the_main_loop.F rather than the ecco version
1310        in ecco type adjoint runs.
1311    o model/src:
1312      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
1313      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
1314      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
1315    o model/src:
1316      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
1317        update output of test experiment bottom_ctrl_5x5.
1318    o pkg/generic_advdiff:
1319      - implement vertical bi-harmonic diffusion (for now, only for T & S and
1320        only explicitly).
1321    o verification/bottom_ctrl_5x5/
1322      update reference output (results changed quite some time ago,
1323      not sure when; but new reference results look ok in terms of grdchk)
1324    o verification/1D_ocean_ice_column/
1325      For verification purposes, the exact adjoint rather than an approx.
1326      should be used (e.g., to comare against F.D. or TLM).
1327      removed autodiff_inadmode*_ad.F routines in code_ad/
1328      Update results/ accordingly.
1329    o pkg/cal:
1330      - change cal_getdate.F so that output date is function of input time only
1331        (less ambiguous, not mixed up with input iteration number).
1332      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
1333    o pkg/diagnostics:
1334      - implement calendarDumps also for stats-diags
1335      - implement calendarDumps also for snap-shot output (negative freq)
1336      - for now, ignores calendarDumps if non-zero phase-lag.
1337    
1338    checkpoint63n (2012/06/04)
1339    o model/src:
1340      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
1341        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
1342      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
1343        similar to calc_r_star.F); update results of experiment internal_wave and
1344        tutorial_global_oce_in_p (affected @ truncation level).
1345    o pkg/shelfice:
1346      - add parameterisation of advective-diffusive flux into the ice shelf
1347        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
1348      - simply eps3/3a computation
1349    o eesupp:
1350     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
1351       between tiles, just fill-in edges assuming locally periodic subdomain) and
1352       add corresponding exchange subroutines (EXCH0);
1353     - new CG-solver version (_EX0) for disconnected-tiles special case.
1354    o model/src (CG-solvers):
1355     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
1356       (similar final residual output and max-Iter number as with standard version);
1357     - allows to store and use lowest-residual solution (standard & _SR versions);
1358     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
1359     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
1360    o eesup/src:
1361     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
1362       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
1363    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
1364    
1365    checkpoint63m (2012/04/27)
1366    o pkg/shelfice:
1367     - account for partical cells in surface level below ice-shelf for hydrostatic
1368       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
1369    o ad test experiments:
1370     - update and rename to "ad_optfile.local" local AD-optfile specific to a
1371       particular adjoint verification experiment (in verification/*/code_ad/)
1372    o pkg/seaice & pkg/exf:
1373     - Part two of ECCO-CLIVAR code merges.
1374       Completes merge of seaice area relax. code.
1375       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
1376       to be set in EXF_OPTIONS.h since this pkg controls its I/O
1377       (and avoids second CPP option in SEAICE_OPTIONS.h)
1378     - change default value of costIceStart & costIceEnd to a valid date.
1379     - add snowPrecip to HSNOW in seaice_growth
1380    o pkg/ptracers:
1381     - move ptracers summary and setup check into separated S/R ; add a check for
1382       valid PTRACERS_Iter0 value (error+stop or just warning).
1383    o pkg/cal (+ pkg/ecco):
1384     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
1385       as input; and for AD, unless both are not differentiable (e.g., k index)).
1386    o model/src:
1387     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
1388       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
1389       temporary set to usingZCoords value (to be changed to F when using shelfice).
1390     - hydrostatic pressure: implement partial cell near the surface also for
1391       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
1392       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
1393    o pkg/ctrl/ctrl_init.F:
1394     - add a formal parameter to s/r ctrl_init_rec to print
1395       xx_$(ctrl_valiable)_file for easier debugging
1396     - move call of cal_* routines into the if-block where they are really
1397       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
1398       to specify a startdate
1399    o pkg/seaice:
1400     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
1401       global_ocean.cs32x15/code versions).
1402     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
1403       verification experiment global_ocean.cs32x15.seaice and update results.
1404    o pkg/exf:
1405     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
1406       (according to useExfYearlyFields).
1407    o pkg/cal:
1408     - move calendar setting & summary (previously in cal_readparams.F) into new
1409       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
1410       length of the simulation is set (after SET_PARMS call); This is an attempt
1411       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
1412     - For safety: keep a record of pkg/cal parameter settings status
1413               to allow to STOP if one pkg/cal S/R is called too early.
1414     - add a stop in all basic pkg/cal subroutines if called before setting is done.
1415     - modify cal_getdate.F: stop when nothing was returned;
1416       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
1417       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
1418    
1419    checkpoint63l (2012/04/04)
1420    o pkg/bbl:
1421      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
1422        update global_with_exf output.yearly.txt file.
1423    o pkg/cal:
1424      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
1425      - remove 2 unsused and very short (1 line only) functions ;
1426      - remove unsused subroutines from AD-Diff list.
1427    o model/src:
1428      - start to implement clean wait to stop in initialization S/R (config_check.F,
1429         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
1430    o folowing PRINT_MESSAGE changes:
1431      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
1432    o pkg/bbl:
1433      - modification so it can work with z*
1434      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
1435      - global_with_exf/input.yearly verification; changes output.yearly.txt
1436    o eesupp/src:
1437      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
1438        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
1439      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
1440        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
1441      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
1442      - when using MPI, always set usingMPI=T ; set default accordingly and stop
1443        if not consistent.
1444      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
1445        argument is zero (in case called within single-thread section).
1446    o pkg/fizhi:
1447        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
1448        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
1449    o pkg/exch2:
1450      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
1451        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
1452      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
1453        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
1454        with bad ones coming from a not-yet-updated halo.
1455        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
1456    o pkg/frazil:
1457        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
1458        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
1459    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
1460    o verification/lab_sea
1461      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
1462      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
1463      * nTimeSteps 3 -> 4
1464      * changed reference output accordingly
1465    o pkg/ctrl:
1466      * fix ctrl_get_gen for xx_sst, xx_sss
1467    o pkg/fizhi:
1468      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
1469        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
1470      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
1471        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
1472        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
1473    o pkg/gmredi:
1474      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
1475    o pkg/fizhi:
1476      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
1477        (old)aces open64 tuv test.
1478    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
1479    o pkg/mom_vecinv:
1480      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
1481        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
1482        with non-lin free-surf).
1483    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
1484      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
1485      some compilers (gfortran 4.6.0 on MacOS)
1486    o momentum:
1487      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
1488        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
1489        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
1490    
1491    checkpoint63k (2012/03/17)
1492    o model/src:
1493       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
1494         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
1495       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
1496         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
1497    o model/src: solve_*diagonal.F
1498       - replace division with multiplication by inverse (similar to original version)
1499         update output of AD exp. global_ocean.90x40x15.
1500       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
1501         to enable the use of the vectorized & differentiable solve_tridiagonal.F
1502       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
1503         vertical advection (to get solve_tridiagonal tested in AD mode).
1504    o pkg/seaice: ECCO-CLIVAR merge:
1505      1. seaice AREA relaxation
1506         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
1507         * runtime flag: SEAICE_tauAreaObsRelax
1508      2. modified global mean cost imbalance code: CPP option
1509          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
1510    o another iteration on solve_*diagonal.F
1511       Make choices independent of AUTODIFF
1512       Default will be the adjoinable vectorized version.
1513       Alternative choices are:
1514       * non-adjoinable original version with low memory footprint:
1515         #define SOLVE_DIAGONAL_LOWMEMORY
1516       * still adjoinable but does not vectorize (k as inner-most loop):
1517         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
1518    o testreport
1519     - add option to use a home made wrapper around "make"
1520     - remove MITGCM_IEEE env. variable (no longer active)
1521    o pkg/shelfice
1522     - improve computation of friction velocity for velocity dependent
1523       exchange coefficients: include velocities into SHELFICEBoundaryLayer
1524       block to average velocities vertically
1525     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
1526    o Modify diagonal solvers, now three versions (upon request):
1527      #ifndef SOLVE_DIAGONAL_AUTODIFF
1528        1. default version (dating back a while ago)
1529      #else /* def SOLVE_DIAGONAL_AUTODIFF */
1530      # ifdef SOLVE_DIAGONAL_KINNER
1531        2. adjoinable version with k-innermost loop (G. Forget)
1532      # else
1533        3. adjoinable vectorized version of 2.
1534      # endif
1535      #endif /* SOLVE_DIAGONAL_AUTODIFF */
1536      All flags are currently set within routines, but could/should be moved to CPP-options.
1537      Array bounds for 1. are as before, for 2.,3. cover the entire domain
1538      (could be changed for 1. too).
1539    o verification/lab_sea (fwd):
1540      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
1541        use 7 categories (except hb87), new solve4temp params (except salt_plume),
1542        constant salinity (=4) or variable salinity (salt_plume) done through
1543        SItracer.
1544    o pkg/seaice:
1545      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
1546      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
1547         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
1548        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
1549        SEAICE_freeze got retired) but already better than previously with
1550        SEAICE_freeze=123456.7 deg.C;
1551      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
1552        (safer multi-threaded setting); always set SEAICEuseEVP;
1553      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
1554        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
1555        stop if multiple specifications for the same coeff; make sure default
1556        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
1557    o pkg/obcs:
1558      - allow to switch to upwind 1rst order advection scheme for the advective
1559        flux computation at the open-boundary; disabled for adjoint built.
1560    o pkg/ptracers:
1561      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
1562      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
1563      - add parameter to decide when to start a tracer; use internal flag to
1564        know which tracer to step-forward; switch this internal flag at the top
1565        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
1566        for adjoint built.
1567    o pkg/seaice:
1568      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
1569      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
1570      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
1571    o pkg/ecco:
1572      - fix writing of output file DiagnosCost_ClimSalt/Theta
1573        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
1574    o pkg/seaice:
1575      - add missing initialisation of COR_ICE array in dynsolver.F
1576      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
1577        compiled either way, and is tested in all exps (multidim was only tested
1578        in lab_sea ad before).
1579      - cosmetic change to prepare for future addition of ITD. no change to results.
1580        no defaults change.
1581      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
1582      - by lack of adequate verification experiments, I further used custom versions
1583        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
1584        should be correct.
1585      - avoid recomputations in ad.
1586    o array initialisation in adjoint mode:
1587      1) pkg/mom_common/mom_calc_ke.F:
1588        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
1589        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
1590        part this initialisation is gone, resulting in Floating Point Exception
1591        (caught by open64 compiler with debug option).
1592      2) model/src/convective_weights.F
1593        set output convectCount over the full array range (instead of doing
1594        an update): this fix a similar issue when called within recomputation (adjoint)
1595        which could by-pass the initialisation (normally done in the caller S/R).
1596    o pkg/seaice:
1597      - final version of turbulent flux params, as agreed at MIT ice meet:
1598           SEAICE_mcPheePiston (default is ~ 0.000875)
1599           SEAICE_mcPheeTaper (default is 0.)
1600           SEAICE_frazilFrac (defualt is 1.)
1601           SEAICE_mcPheeStepFunc (default is false)
1602      - changes results at trunction error level
1603      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
1604    o added pkg/frazil:
1605      - see frazil_description.tex for details
1606      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
1607    o pkg/shelfice/shelfice_thermodynamics.F
1608      - fix exponents for velocity dependent exchange coefficients: change
1609        from 2/3(=0) to 0.66666666666666667
1610      - move computation of velocity dependent exchange coefficients into
1611        separate loop, so that it applies to both thermodynamics
1612      - move some divisions by constants out of loops
1613    
1614    checkpoint63j (2012/02/16)
1615    o pkg/seaice:
1616      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
1617      - SItracer:  added run time params, and allow coupling to ocn salinity.
1618    o pkg/seaice: remove (almost) all divisions by constants within loops
1619      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
1620      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
1621      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
1622      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
1623    o pkg/seaice :
1624      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
1625        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
1626      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
1627      - add permanent SItflux diag that corresponds to TFLUX but includes
1628        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
1629      - allow activation/testing of a fix for suspected missing term in
1630        ocn-ice heat budget (to be confirmed). To test this, you want to
1631        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
1632        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
1633      - no change in results, fwd or ad.
1634    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
1635      - switch to variable freezing point.
1636           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
1637      - bug fix : the sublimation term that was missing is now activated.
1638           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
1639      - bug fix : flooding sign term for SIsal0.NE.0.
1640           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
1641    o pkg/seaice:
1642      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
1643        is now the default, and the old default constant freezing point is recovered
1644        with SEAICE_tempFrz0    = -1.96,
1645             SEAICE_dTempFrz_dS = 0.,
1646      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
1647      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
1648      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
1649        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
1650      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
1651        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
1652      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
1653        seaice_growth r149 for legacy branch (no results change).
1654      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
1655        from I. Fenty).
1656      - results did not change except for global_ocean.cs32x15, mostly due to the
1657        switch to variable freezing point (see above item for detail).
1658    o pkg/thsice:
1659      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
1660        seawater freezing in thsice_calc_thickn (not used).
1661    o pkg/seaice: turbulent flux term specification via run time params.
1662      - replace CPP switches with run time switches to facilitate testing
1663      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
1664                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
1665      - added runtime parameter : SEAICEturbFluxFormula
1666      - move Mcphee constants to SEAICE_PARAMS.h
1667      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
1668                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
1669                 remove seaice_summary call (moved to seaice_init_fixed)
1670      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
1671        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
1672      - seaice_summary.F : add missing report of read turbulent flux term set up
1673                           and SITRACER.
1674      - seaice_check.F : check range; inform and stop if retired CPPs are used
1675                         (incl. SEAICE_AGE).
1676      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
1677             CPP switch, same computation as before for the different options.
1678      - change results at the truncation level.
1679    o pkg/seaice:
1680      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
1681        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
1682        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
1683      - update verification/*/input*/data.seaice:
1684        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
1685        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
1686        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
1687        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
1688    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
1689      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
1690        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
1691        difference in results only due to machine truncation.
1692      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
1693        MaykutPolySatVap; keep MIN_LWDOWN.
1694      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
1695      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
1696        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
1697    o pkg/salt_plume:
1698      - isolate saltPlumeFlux array exch into a specific S/R called from
1699        do_oceanic_phys.F
1700      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
1701    o verification:
1702      - move untested set-up to MITgcm_contrib/verification_other.
1703    o pkg/seaice:
1704      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
1705    o pkg/seaice:
1706      - seaice_solve4temp.F (keeping results unchanged):
1707        * add 2 future run-time params to select which saturation vapor pressure
1708          formula is used and how post-iteration fluxes are set.
1709          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
1710        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
1711          the linearized expression to stay consistent with tsurf finding.
1712      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
1713        can be < 0.
1714    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
1715      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
1716        conductive heat flux F_c , and add it explicitly when updating tsurf as
1717        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
1718        so that now F_ia has a consistent meaning through the entire routine.
1719        This causes differences at truncation level: update output of fwd exp.
1720        global_ocean.cs32x15.seaice.
1721    o pkg/seaice:
1722      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
1723        of arrays, sign/direction of fluxes; no effect on results.
1724      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
1725        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
1726        note: this should have been done before changing celsius2K default.
1727      - to keep results unchanged, add back old value of celsius2K in verification
1728        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
1729      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
1730        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
1731        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
1732        freezing temp is consistent with value in seaice_growth.F ; this causes
1733        differences at machine truncation level: update lab_sea AD output (3/4).
1734    o pkg/seaice:
1735      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
1736        and climsst/sss even when using seaice (to prevent calculation that might
1737        use SST on land); does not affect any verification exp.
1738      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
1739        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
1740    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
1741      over land (non-legacy code)
1742    o vectorize salt_plume package:
1743      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
1744      - this code computes plumebk everywhere (also over land), thus requires
1745        code to avoid divisions by zero and catch the case of kLev=Nr.
1746      - efficiency of salt_plume_frac is still sub-optimal
1747    o tools (genmake2):
1748      - fix makefile NAME specification (option: -makefile NAME) by adding
1749        "-f $MAKEFILE" in few places where it was missing including makedepend
1750        command (contribution from Paul).
1751    
1752    checkpoint63i (2012/01/24)
1753    o model/src:
1754      - add factorized versions of some EOS code to find_rho.F,
1755        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
1756    o model/src:
1757      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
1758      - change default celsius2K from 273.16 to 273.15
1759      - to keep results unchanged, add back old value of celsius2K in verification
1760        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
1761         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
1762    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
1763      to make TAF generate vectorizable code
1764    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
1765       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
1766       have flags that do this more efficiently.
1767    o pkg/diagnostics/diagstats_calc.F
1768      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
1769    o pkg/obcs (with exch2):
1770      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
1771        and remove code (in obcs_readparms.F) which was based on EXCH of indices
1772        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
1773    o pkg/exf and seaice exp:
1774      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
1775        so that switching off area & heff advection flags does not affect results.
1776      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
1777      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
1778        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
1779        results of verification experiments: 1D_ocean_ice_column(fwd),
1780        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
1781        and offline_exf_seaice (all 4).
1782    o pkg/seaice:
1783      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
1784        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
1785      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
1786        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
1787        not multi-dim advection;
1788      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
1789        SHORTWAVE_HEATING #undef.
1790    o optim: make Makefile more robust (?)
1791    o pkg/obcs:
1792      * fix treatment of obcs_read_pickup for TAF
1793    o pkg/shelfice:
1794      * add missing initialisation of num_shifwflx
1795      * new adjoint verification exp. for isomip
1796      * change Prandtl and Schmidt numbers from generic formulations
1797        (in terms of model diffus. and visc.) to separate runtime
1798        parameters, with Holland and Jenkins (1999) default values.
1799    o pkg/exf (interpolation):
1800      - extended input field (2 rows) near the N & S poles:
1801        * fill in with the symetric value (when even Nb of data in longitude)
1802        * add average value at the poles only for scalar quantities ; for vector
1803          component interpolation, skip the averaging and keep duplicated values,
1804          unless the 2 components have same location (uvInterp=T) in which case
1805          interpolate the 2 components together using S/R EXF_INTERP_UV.
1806      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
1807        together: this allows to account properly for local orientation when
1808        averaging at N & S pole.
1809      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
1810        exf-interpolation near N & S poles. Undef by default.
1811      - add debug check/print on 1rst iter if debugLevel >=2.
1812    o pkg/exf:
1813      - change masking flags definition (no longer "parameter"), put them in
1814        common block and set them in S/R EXF_INIT_FIXED.
1815      - change recognized masking flag from s,u,v to c,w,s since the mask
1816        to use (maskC,W,S) depends on position on model grid and has little to
1817        do with scalar/vector difference; fix masking if using P-coordinates.
1818      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
1819        and update results of exp. global_with_exf (x2).
1820      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
1821    o pkg/obcs
1822      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
1823    o pkg/exf (interpolation):
1824      - assume periodicity in X only if input field cover full longitude range.
1825      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
1826        and should vectorise).
1827      - fix input lat of the 2 added row (in case we provide N.pole data).
1828    
1829    checkpoint63h (2011/12/30)
1830    o pkg/seaice:
1831      - change declaration of UVM from _RL to _RS in order to get B-grid
1832        uIce,vIce monitor when _RS = real*4
1833    o pkg/offline:
1834      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
1835      - compute vertical velocity if not read from file (switch on exactConserv
1836        & staggerTimeStep);
1837      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
1838    o verification:
1839      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
1840        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
1841        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
1842      - update output of exp. global_ocean.cs32x15.viscA4 after changing
1843        grid-file angles (used here for coriolis-3d);
1844      - remove (or gzip) few files not needed to run fizhi-cs experiments.
1845    o pkg/exf (vector interpolation):
1846      - rotate vector component toward local grid-axis orientation using grid-angles
1847        (stored in GRID.h) instead of locally computed rotation angle; keep old code
1848        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
1849    o pkg/seaice:
1850      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
1851        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
1852    o pkg/PKG_OPTIONS.h files:
1853      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
1854        outside of the #ifdef ALLOW_THISPKG / #endif block.
1855      - update verification/*/code/PKG_OPTIONS.h files.
1856    o add a verification experiment (offline_exf_seaice/input.seaice) that test
1857      the B-grid LSOR solver
1858    o pkg/seaice: sort out emissivity and long wave radiation step 2:
1859      - add emissivity for snow and ice as new run-time parameters
1860        (unfortunately) that default to the corresponding exf values; this
1861        changes results in most verification experiments so that for backward
1862        compatibility these parameter have to be set explicitly to inconsistent
1863        values (ugly);
1864      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
1865        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
1866        until we agree how to handle this bug properly
1867    o pkg/exf (interpolation):
1868      - add a set of run-time param ({inputfield}_interpMethod), one for
1869        each interpolated input field, to select the interpolation method
1870        with a value of zero switching off the interpolation;
1871      - print interpolation parameters to standard output;
1872      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
1873        (to use instead runoff_interpMethod=0 in data.exf).
1874      - simplify default setting of interpolation parameters (for all fields,
1875        set position to match model grid cell-center position, leading to trivial
1876        interpolation in case of regular Lat-Lon grid) and fix for the case of
1877        non-uniform delY.
1878    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
1879       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
1880       this factor is absolutely required, because the lw exitance (= out-going
1881       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
1882       where the reflectivity rho = 1-emissivity for conservation reasons. Once
1883       this is established, we can remove the CPP-Flag (if we want to).
1884    o pkg/seaice:
1885      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
1886        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
1887      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
1888        what the name implies (and not emissivity*BoltzmannConstant), this means
1889        the old default value of 5.5e-8 now means
1890        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
1891        S/R exf_readparms
1892      - FV-discretization of the B-grid LSOR solver, turn on with
1893        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
1894        of the calling routine dynsolver, so that B and C-grid code look a
1895        little more alike.
1896      - fix index bugs in ostres.F (B-grid code)
1897    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
1898    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
1899      default for SEAICE_emissivity, if useEXF; requires setting a wrong
1900      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
1901      backward compatiblity
1902    o model/src: use sigmaR in calc_ivdc
1903    
1904    checkpoint63g (2011/12/16)
1905    o pkg/seaice/seaice_growth.F:
1906      fix heat conservation of the coupled ocean-seaice system.
1907      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
1908      solid vs liquid water treatment is resolved via QNET.
1909    o pkg/seaice/seaice_growth.F:
1910      add missing term for sublimation in saltFlux, which was breaking conservation.
1911    o pkg/seaice/seaice_model.F:
1912      Remove this patholigical case treatment in evolution branch,
1913      where it is un-necessary and breaks conservation.
1914      Update global_ocean.cs32x15/results accordingly for
1915      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
1916    o model/src:
1917      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
1918      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
1919    o pkg/obcs:
1920      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
1921      tendency for temperature and salinity that is then applied to update
1922      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
1923      horizontal advection and diffusion contributions on the boundary (in
1924      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
1925      removing the mask in S/R timestep_tracer. The advantage of this approach is
1926      that the updated tracer values include contributions from the surface
1927      forcing and vertical diffusion.
1928      This modification changes exp4.stevens because of vertical diffusion.
1929    o model/src:
1930      change non-curvilinear grid setting to also work with exch2 + blank tiles:
1931      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
1932        face dimensions.
1933      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
1934        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
1935        and INI_SPHERICAL_POLAR_GRID.
1936      change test-experiment global_ocean.90x40x15:
1937      - split the domain in many more tiles (9x4 tiles of 10x10 each);
1938      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
1939      - update results of both test (std & dwnslp).
1940    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
1941       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
1942    o model/src:
1943      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
1944        and fix initialisation when using sigma-coords.
1945    o model/src:
1946     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
1947       to their current value at the beginning of forward_step.F": add a new run-time
1948       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
1949     - set doResetHFactors=T in the following test exp:
1950        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
1951        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
1952        and tutorial_global_oce_in_p (nonLinFS in p)
1953    o pkg/ecco
1954      - added IES cost term
1955    o verification/advect_xz
1956      - scale down the depth by 1/100 (from 200 km to just 2.km)
1957      - add secondary test using divergent flow, r-star and implicit vertical advection.
1958      - add note (check_conserve_TS.txt) and matlab script to check global
1959        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
1960    o pkg/rbcs:
1961      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
1962    o pkg/obcs (Stevens BCs):
1963      - fix various problems in the phase speed computations of the Stevens
1964        boundary conditions:
1965        - sign error for western and southern boundaries,
1966        - time tendencies were underestimated by factor of dTracerLev and some just
1967          zero (for multidim advection schemes) -> now estimate time tendencies
1968          from difference between previous (n) time level and the one before (n-1);
1969          this requires storing a field per tracer per boundary, also in the pickup
1970          files.
1971        - replace deltaTmom in cflMer/Zon computation with dTracerLev
1972        - set default phase velocity to cflMer/Zon
1973      - update verification experiment exp4.stevens
1974    o pkg/generic_advdiff (implicit_r):
1975      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
1976        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
1977      - fix implicit vertical diffusion or advection with NonLin FreeSurf
1978        (was using current recip_hFacC instead of future recip_hFacC): set future
1979        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
1980        solver S/R ;
1981      - fill diagnostics of vertical advective fluxes (computed from tendency)
1982        when using implicit vert. advection;
1983      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
1984         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
1985         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
1986         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
1987    o pkg/diagnostics:
1988      - add diags for T & S tendency which goes through Adams-Bashforth.
1989    
1990    checkpoint63f (2011/11/30)
1991    o pkg/obcs/obcs_calc_stevens.F:
1992      - join some loops to reduce number of if-statements
1993      - fix a bug in code for northern and southern boundaries.
1994    o pkg/seaice/seaice_init_varia.F
1995      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
1996        caused zero ice-velocities for the B-grid code
1997    o pkg/seaice/seaice_init_fixed.F
1998      - fix a bug in the initialisation of the second metric terms
1999        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
2000      - this affects all seaice configurations with useCurviLinearGrid = .true.
2001        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
2002        = .true. (default)
2003      - the only verification experiment affected is global_ocean.cs32x15:
2004        icedyn, seaice, and seaice_dynmix (AD)
2005    o pkg/thsice/thsice_diagnostics_state.F
2006      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
2007        not contain garbage that can lead to surprises in diagstats_calc.F
2008    o model/src:
2009      - move bi,bj loops inside INTEGR_CONTINUITY ;
2010      - call INTEGR_CONTINUITY directly from forward_step.F
2011        (previously called from momentum_correction_step.F)
2012      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
2013        forward_step.F and pkg/ecco/the_main_loop.F
2014    o model/src/do_oceanic_phys.F:
2015      - reset addMass to zero only if useICEFRONT ;
2016      - separated k-loop for rhoInSitu calculation ;
2017      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
2018        and at constant T,S (= WdRHOdP);
2019      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
2020        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
2021        transport of locally-referenced potential density);
2022        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
2023    o gluemnc:
2024      - replace ncrcat with ncks when adding variables to *.glob.nc
2025      - change the way variables without record dimensions are handled so that
2026        files that have variables with and without record variables can be glued:
2027        add a record dimension with a new unique name to be able to differentiate
2028        between variable with and without a-prior record dimensions. Remove
2029        this record dimension before adding the variable to the *.glob.nc file.
2030        This procedure automatically works also for grid.*.nc files that do not
2031        have any record dimension.
2032    o verification/cpl_aim+ocn:
2033      - generate new reference output on baudelaire (gfortran, mpich2) (previously
2034        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
2035    o pkg/obcs/obcs_calc_stevens.F:
2036      - add code for northern and southern boundaries.
2037      - reorder some loops to save some operations and so that drFBar can be scalar
2038    o model/src:
2039      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
2040        truncation) and add diagnostics for Adams-Bashforth tendency increment.
2041      - update test-exp. AD output:
2042        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
2043      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
2044        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
2045        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
2046        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
2047        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
2048        tutorial_plume_on_slope.
2049    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
2050      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
2051      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
2052      does not even come with an F77 compiler anymore, this should not be
2053      a limitation
2054    
2055    checkpoint63e (2011/11/06)
2056    o pkg/seaice adjoint of LSR:
2057      - substantially rework STORE dirs.
2058      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
2059        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
2060        and only perform SOLV_MAX_FIXED adjoint iters.
2061        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
2062        always goes to same record, meaning that the last forward field will be
2063        the one used in the adjoint - an approximation.
2064      - now produces non-zero LSR-related gradients, and acceptable gradients for
2065        An's zonal (x-z) test case (to be checked in)
2066      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
2067        (but these are screwed up by the thermodynamics in the first place);
2068        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
2069        output_adm.txt also reflects changes to seaice_lsr
2070      - global_ocean.cs32x15:
2071        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
2072          (output_adm.seaice.txt was updated)
2073        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
2074          (output_adm.seaice_dynmix.txt)
2075    o test-exp. exp4+stevens:
2076      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
2077    o pkg/seaice (lsr solver):
2078      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
2079        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
2080      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
2081      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
2082        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
2083      - compute (with new S/R) and print initial (+ free-driff sol. if available)
2084        and final residual of linearised system.
2085    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
2086      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
2087    o pkg/obcs: Stevens BCs (still only for east and west)
2088      - fix Stevens BCs by using intermediate velocities of previous
2089        time step as "baroclinic" contribution rather velocity of one grid cell
2090        inside the boundaries; more consistent but makes the entire treatment
2091        more complicated, requires new pickup files and two new S/Rs:
2092        obcs_copy_uv_n and obcs_save_uv_n
2093        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
2094        (undefined by default)
2095      - silently move computation of some grid factors into separate loops to
2096        save some recomputations
2097      - add a hack for non-linear free surface
2098      - add a verification experiment to exp4 that tests this code
2099    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
2100    
2101    checkpoint63d (2011/10/25)
2102    o pkg/obcs + seaice-dynamics:
2103      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
2104        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
2105        values (consistent with an implicit method).
2106      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
2107        return to older implementation (same results as before); note that none of
2108        the "experimental" OBCS_SEAICE options are implemented in the new version.
2109      - switch test exp. seaice_obcs to use new version (update output).
2110    o pkg/seaice:
2111      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
2112      - add parenthesis in Water-Ice drag calculations (evp & lsr);
2113      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
2114        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
2115      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
2116        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
2117    o pkg/layers:
2118      - Include potential density as new coordinate (Thanks to David Munday)
2119    o pkg/dic:
2120      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
2121        carbonate computation/output to CALC_PCO2_APPROX
2122    o pkg/generic_advdiff
2123      - make TAF generate code that vectorizes:
2124        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
2125    o model/src:
2126      - improve vectorization also for adjoint code of
2127        solve_tridiagonal and solve_pentadiagonal. As this requires up to
2128        5 new 3D-fields, this code is only turned on for the combination of
2129        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
2130        for singular matrix check (only for TARGET_NEC_SX).
2131      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
2132        ALLOW_AUTODIFF. This flag now needs to be set outside of
2133        solve_tri/pentadiagonal.F
2134    o pkg/exf:
2135      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
2136        optional namelist EXF_NML_OBCS).
2137      - add many debug-print (to trace down where pkg/cal error msg comes from)
2138    o pkg/mom_vecinv/mom_vi_hdissip.F
2139      - rearrange loops so that vectorization is improved and in particular
2140        the adjoint routine vectorizes. The code is a little longer now, but I
2141        think easier to read.
2142        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
2143    o pkg/seaice:
2144      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
2145    o pkg/exch2:
2146      - alternative code (without tile x tile matrix) for cumulated (global) sum;
2147        used as default; keep using matrix version in adjustment.cs-32x32x1.
2148    o tools/build_options:
2149      - after merging some MPI and/or multi-threads specific optfiles so that
2150        the modified default optfile support both built (using genmake2 -mpi
2151        for the MPI built, using genmake2 -omp for OpenMP built),
2152        move now obsolete optfiles to tools/build_options/unsupported/
2153       (add copy of email sent to support list in doc/optfiles_changes.txt)
2154    
2155    checkpoint63c (2011/09/28)
2156    o pkg/ebm:
2157      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
2158        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
2159    o pkg/seaice (SItracer pickup)
2160    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
2161      To be done:
2162      - thorough testing of missing fields in S/R seaice_read_pickup
2163      - thorough matching between generic tracers and specific fields used
2164        (e.g. volume-weighted age, area-weighted age, salinity, ...)
2165    o pkg/grdchk:
2166      - all procs calculate and print finite-difference gradient (for testreport)
2167      - change description output used by testreport;
2168      - AD testing: also compare and report Finite-difference gradient;
2169        => update all output_adm*.txt
2170    o test exp. global_ocean_ebm:
2171      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
2172        and turn on exactConserve; update (fwd) output.
2173    o pkg/seaice (LSR):
2174      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
2175      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
2176        * identical results with non-CS topology (but save up to half of EXCH calls)
2177        * no much changes in cs-32 verification tests since no ice at face edges
2178         (differences due to convergence criteria, since nb of iterations changed)
2179        * expect some differences on lat-lon-cap grid.
2180        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
2181    o pkg/exch2:
2182      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
2183        many tiles); until alternative coding is added, just add a stop.
2184    o pkg/kpp:
2185      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
2186        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
2187    o optfiles:
2188      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
2189        into corresponding standard one, which now support different build:
2190        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
2191      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
2192    o pkg/obcs (seaice):
2193      - add missing EXCH for uIce,vIce after applying OBCS;
2194      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
2195        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
2196        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
2197      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
2198      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
2199        and eedata.mth for MPI and mutlti-threaded testing.
2200    o pkg/flt:
2201      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
2202      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
2203      - fix pickup and trajectories + profiles output with multi-threads;
2204      - add parameter to select group of fields to write along trajectory and
2205        profile (default unchanged);
2206      - only call PORT_RAND* function when flt_noise <> 0;
2207      - add multi-threaded test for verification exp. flt_example.
2208    o eesupp/src:
2209      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
2210      - USE_OMP_THREADING: check that number of threads (from eedata) matches
2211        actual number (from env.var. setting).
2212    o pkg/ebm:
2213      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
2214      - add multi-threaded test for verification exp. global_ocean_ebm
2215    
2216    checkpoint63b (2011/08/29)
2217    o pkg/ebm:
2218      - fix sign of runoff;
2219      - update directly forcing fields (Qnet,EmPmR) to use standard
2220        external_forcing_surf.F (remove ebm_forcing_surf.F);
2221      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
2222      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
2223        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
2224      - update global_ocean_ebm parameters file data and update output (fwd+ad).
2225    o verification/matrix_example:
2226      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
2227        MPI and mutlti-threaded testing.
2228    o pkg/matrix:
2229      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
2230      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
2231      - fix for multi-threaded (remove DATA statement);
2232      - use standard DIFFERENT_MULTIPLE function;
2233      - add MATRIX_OPTIONS.h
2234    o verification/matrix_example:
2235       To allow to split the domain in several tiles, change the domain size
2236        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
2237        Western side) of land points.
2238    o (*_)write_pickup:
2239      - fix few bugs in mypackage_read/write_pickup.F
2240      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
2241        array of length 1 (was caught by compiler syntax-check).
2242    o pkg/diagnostics (velocity potential solver):
2243      - fix initialisation of main diagonal matrix (for overlap values)
2244    o tools/build_options:
2245      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
2246        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
2247      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
2248        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
2249        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
2250        and use "-devel" testreport option for standard testing on baudelaire.
2251    o pkg/grdchk:
2252      - Assume that all gradient-check position are within the same tile
2253        corresponding to global indices (iGloTile,jGloTile) and that
2254        positions (i,j indices or nbeg) are local to this tile;
2255      - set tile local-indices and proc. number according to tile global-indices;
2256      - remove grdchkwhichproc from namelist (retired param);
2257      - send adjoint gradient to all procs so that all procs print it to STDOUT;
2258      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
2259    o adding package bbl (Bottom Boundary Layer)
2260      description in MITgcm/pkg/bbl/bbl_description.tex
2261      example/test experiment in MITgcm_contrib/bbl
2262    o adjoint verifications
2263      - changed 5 experiments to multi-tiles
2264        * global_ocean.90x40x15
2265        * obcs_ctrl
2266        * offline_exf_seaice
2267        * tutorial_dic_adjoffline
2268        * tutorial_tracer_adjsens
2269        changed reference output for those that crossed tile boundaries
2270        (changed choices of gradient check positions)
2271      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
2272      - temporary bug fix in grdchk_loc.F for obcs
2273    o genmake2 & testreport
2274      - add target "obj" (just for OBJFILES files) to Makefile;
2275      - add option to specify FEXTRAFLAGS on command line.
2276    o pkg/mypackage:
2277      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
2278    
2279    checkpoint63a (2011/08/02)
2280    o pkg/diagnostics (velocity potential):
2281      - fix velocity-potential calculation when using OBCS: balance net inflow
2282        at each level (new S/R OBCS_DIAG_BALANCE).
2283      - fix some of the problems with OBCS in stream-function calculation.
2284    o pkg/exf/exf_readparms.F
2285      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
2286        EXF_NML_OBCS) more consistent, so that you need not have these lists
2287        in data.exf when they are not used.
2288    o optim/optim_readdata.F:
2289      - add some output about obcs variables that might help debugging
2290      - add a check about nvarlength
2291    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
2292    o pkg/diagnostics (velocity potential):
2293      - fix mask for OBCS (still problems in stream-function with OBCS);
2294      - add specific parameter (default = main code CG2D params) for solver;
2295      - in case of poor convergence, use solution corresponding to lowest residual.
2296    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
2297      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
2298      and should be avoided where possible.
2299    o model/src (rStar):
2300      - include r* effect on reference-state (PhiRef) in totPhiHyd
2301        (so that it's really the potential anomaly at the cell center);
2302        affect solution only if z* with full pressure in EOS.
2303      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
2304        update output (because of z* in totPhiHyd and viscA4 changes);
2305      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
2306        @ constant r) until interpolation at constant r is implemented.
2307    o pkg/diagnostics
2308      - fix RCENTER diagnostics in case cell center is not at interface middle
2309    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
2310      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
2311      that THETA and SALT are "conservative temperature" and "absolute
2312      salinity"
2313    o pkg/ctrl
2314      - fix computation of endrec in s/r ctrl_init_rec
2315      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
2316    o pkg/seaice/seaice_growth.F
2317      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
2318        remove then obsolete STORE directives
2319      - fix STORE directives for tice and tices, so that only the
2320        appropriate part of the fields are stored (and not the entire
2321        field); update global_ocean.cs32x15.seaice AD output.
2322      - cosmetic changes: adjust CPP flags and indentation for better
2323        legibilty
2324    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
2325      Chris Wilson)
2326    o pkg/gmredi:
2327       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
2328       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
2329    
2330    checkpoint63  (2011/07/11)
2331    o pkg/exch2:
2332     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
2333     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
2334       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
2335       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
2336    o pkg/diagnostics:
2337     - deal with pairs of post-processed diags which are computed together; in
2338       particular, re-order list of diags within 1 file to save 2nd computation.
2339     - add S/R to compute velocity stream-function (called after velocity-potential
2340       calculation) from divergence free transport -> new diagnostics "PsiVEL".
2341     - add parameter to select grid-point location where PsiVEL == 0.
2342    o eesupp/src:
2343       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
2344       (specific S/R needed with exch2 topology - for now, just print an error msg)
2345    o pkg/shelfice
2346     - Implement friction velocity-dependent transfer coefficients following
2347       Holland and Jenkins, JPO, 1999
2348       Original code by M. Losch with small modifs.
2349       Enable with CPP option SHI_ALLOW_GAMMAFRICT
2350       and runtime flag SHELFICEuseGammaFrict
2351    o verification lab_sea & global_ocean.cs32x15:
2352     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
2353       does not miss some dependencies (but is slower) and also works with many files
2354       (default makedepend limitation for AD built).
2355     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
2356    o pkg/diagnostics:
2357     - add run-time parameter "useMissingValue" (def=False) to fill land-point
2358        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
2359       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
2360     - Extend the use of "missing_value" setting from data.diagnostics for the case
2361       of counter-diagnostics (where fraction-weight is zero). This applies both to
2362       MNC and MDS output files.
2363    o pkg/seaice/seaice_growth.F:
2364      - add 'a priori' cap of latent heat flux based on actual mass considerations
2365        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
2366        non-legacy seaice_solve4temp.
2367      - add diagnostic of the residual sublimation freshwater flux (the freshwater
2368        flux taken from the ocean if the total actual latent heat fluxes exceed
2369        the maximum)
2370      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
2371       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
2372      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
2373       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
2374      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
2375      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
2376    o verification 1D_ocean_ice_column:
2377       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
2378       update results
2379    o pkg/diagnostics:
2380     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
2381       which are not filled-up but computed from other diags ; In this case, the mate
2382       diag points to the primary (filled-up) diag to used for post processing.
2383     - Update Velocity-potential computation using post-processed diag framework.
2384     ==> Change the ordering of fields and time-periods in MDS output file
2385       when using periodic averaging: now writes one time record with the full set
2386       of fields for this time period, then the next time reccord (it used to be
2387       one field with the full set of time records then the next field).
2388         Note: this is now similar to NetCDF (MNC) output file. <==
2389    
2390    checkpoint62z (2011/06/21)
2391    o adjoint monitor:
2392     - Add adjoint monitor output for packages exf, seaice
2393       and update relevant testreport output
2394    o pkg/seaice:
2395     - re-order diags inits so that they appear in order in available_diagnostics.log
2396     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
2397       area/heff/hsnow preceeding thermodynamic growth/melt.
2398     - modified diag: SIdA; output actual effect, as the description states.
2399     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
2400     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
2401       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
2402        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
2403     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
2404     - added diagnostics for seaice generic tracers (SItr*).
2405     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
2406     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
2407     I. Fenty: 18-Jun-2011:
2408     Minor changes to seaice package:
2409     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
2410        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
2411       - Differentiated "regularization variables" from "floor variables"
2412        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
2413        * hiceMin became SEAICE_hice_reg (old hiceMin)
2414          (with _reg meaning regularization variable)
2415       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
2416        so as to ensure energy conservation when going between phases
2417      - A22 was not used anywhere
2418     2) Changed regularization procedure for heffActual and hsnowActual to ensure
2419        well-boundedness and smooth adjoint in seaice_growth.F
2420     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
2421        because the old regularization always set heffActual >= 0.05 cm
2422     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
2423        on AREA when HEFF > 0.
2424      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
2425        requiring that DISABLE_AREA_FLOOR *not* be defined
2426     Affected verifications:
2427      - 1D_ocean_ice_column (output.txt output_adm.txt)
2428      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
2429    o pkg/diagnostics:
2430      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
2431      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
2432        (was _RL, now integer) with option = 0 to retrieve all levels.
2433      - add pieces of code to compute velocity potential at each level (new diagnostics
2434        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
2435        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
2436      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
2437        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
2438        and in diagnostics_fract_fill.F (do not need a valid pointer for the
2439        diagnostics counter-mate); check that definition of counter-diagnostic
2440        includes a valid counter-mate (in diagnostics_set_levels.F).
2441    o model/src (rStar):
2442      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
2443        affect solution only if z* with full pressure in EOS;
2444        update output of test-exp global_ocean.90x40x15.
2445    o pkg/seaice:
2446      - introduce siEps=1e-5 parameter
2447      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
2448      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
2449      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
2450        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
2451        as well as ice cover age and ridging index (attached to AREA).
2452        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
2453        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
2454        Up to SItrMaxNum=3 tracers can be used simultaneously.
2455    o pkg/salt_plume:
2456      -introduce SPsalFRAC run time parameter that sets the fraction of the
2457       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
2458       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
2459    o model debug options:
2460      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
2461        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
2462      - Refine debug-msg printing selection (3 new levels):
2463        debugMode  : controls printing of debug messages (sequence of S/R calls).
2464        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
2465         debLevZero =  0 ; /* level of disabled aux. msg printing */
2466         debLevA =  1 ; /* level of minimum  aux. msg printing */
2467         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
2468         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
2469         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
2470         debLevE =  5 ; /* level of extensive debug printing */
2471        New debugLevel default: with default debugMode value (=F),
2472          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
2473          and if debugMode=T, default debugLevel = 4 (debLevD).
2474        Relation with previous settings:
2475         debLevB (=2) corresponds to former debLevA (=1)
2476         debLevD (=4) corresponds to former debLevB (=2)
2477        Note:
2478         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
2479         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
2480            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
2481      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
2482        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
2483    o pkg/obcs:
2484      - change OBCSfixTopo default from True to False (should not change the results);
2485        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
2486    o pkg/thsice:
2487      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
2488        2nd layer seaice sublimation (unlikely to happen)
2489      - use Interior mask for OBCS in thsice_advection.F (similar to what is
2490        done in gad_advection & seaice_advection).
2491    o adjoint:
2492      bug fix spotted by Gael Forget:
2493      seaice_advection and thsice_advection still had
2494      legacy CPP options to avoid CS corner updates for adjoint
2495    o pkg/seaice:
2496      => Change some of the defaults (2011/05/29):
2497         - change SEAICEuseFluxForm default (from False to True)
2498         - change DIFF1 default (from 0.004 m/s to 0. m/s)
2499         And print warnings if DIFF1 is not set in data.seaice and centered
2500          avection scheme is used without any diffusion.
2501      also:
2502      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
2503      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
2504      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
2505        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
2506        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
2507      update results of test exp.:
2508         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
2509             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
2510             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
2511         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
2512         seaice_obcs: output (SEAICEuseFluxForm=T)
2513      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
2514          for standard fwd & AD lab_sea tests (to keep the same output).
2515    o pkg/seaice/seaice_growth.F:
2516      - use Ian Fenty's capping formulas for actual ice
2517      thickness thoughout EVOLUTION branch.
2518      - put treatment pathological case #2) in CPP brackets
2519      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
2520      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
2521    o pkg/seaice:
2522      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
2523      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
2524      also pass fac as a param, which can be 1. (to update the tendency
2525      field) or the time step (to update the field itself).
2526      - seaice_advdiff.F: for multidim, call seaice_diffusion with
2527      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
2528      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
2529      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
2530      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
2531    o pkg/seaice:
2532      diffusion with centered advection scheme (diffus.F & advect.F):
2533      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
2534        to just compute the laplacian of input-field.
2535      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
2536      - fix flux-form version in diffus.F to conserve tracer.
2537      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
2538       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
2539    
2540    checkpoint62y (2011/05/26)
2541    o pkg/seaice:
2542     - seaice_growth.F : in EVOLUTION branch, always include
2543       a_QSWbyATM_cover in qnet (as it should be).
2544     - verification/global_ocean.cs32x15 : update results accordingly
2545       (output.seaice.txt output_adm.seaice.txt).
2546    o pkg/seaice + obcs:
2547     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
2548       equivalent of assuming no tracer gradient outside the OB region.
2549       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
2550     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
2551       after changes above);
2552     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
2553       only at OB location (instead of over a band of OLx width).
2554    o pkg/seaice:
2555     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
2556       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
2557    o pkg/obcs:
2558      - split header file "OBCS.h" into 4 separated files:
2559        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
2560       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
2561         (contain no conditional statement which depends on OBCS options).
2562      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
2563        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
2564    o ctrl, cost, grdchk & autodiff pkgs:
2565      - make options file more standard (like other {PKG}_OPTIONS.h file but
2566        with AD_CONFIG.h); clean-up some of the included header files.
2567    o pkg/obcs:
2568      - do not mask tracer when applying OB (tracer == 0 could generate problems)
2569      - apply tracer OB values to tracer field only at OB location (instead of
2570        over a band of OLx width)
2571      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
2572      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
2573        obcs_apply_tloc.F & obcs_apply_sloc.F
2574    o obcs in model/src:
2575      - call OBCS_APPLY_W only if NonHydrostatic.
2576      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
2577      - reset dEtaHdt and wVel to zero outside OB interior region ;
2578      - leave tracer unchanged outside OB interior region: This has no effect
2579        on the solution but just to prevent unrealistic tracer value outside OB.
2580      - zero out velocity outside OB interior region: This has no effect on
2581        the solution but just to prevent unrealistic velocity outside OB.
2582    o obcs and non-lin free-surf:
2583       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
2584       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
2585       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
2586       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
2587       update results of test-exp. exp4(nlfs).
2588    o exp4 (nlfs) test-exp:
2589       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
2590       with NonLin-FreeSurf); update output.nlfs.txt
2591    o obcs and 2d/3d solver norm:
2592       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
2593       and outside OB interior region (will allow to place OB further inside the
2594       domain). Depending on the domain, can affects cg2d-Norm (previous
2595       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
2596       and cg3d-Norm (previous Norm was computed before canceling OB terms),
2597       e.g. in tutorial_plume_on_slope.
2598      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
2599    o pkg rbcs:
2600      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
2601      - add capability to apply relaxation to horizontal velocity uVel & vVel.
2602    o pkg/grdchk: add gradient check for control variable xx_shifwflx
2603    o pkg/shelfice/shelfice_init_fixed.F
2604      fix CPP-flag combinations
2605    o pkg/seaice: Merge iceage code of Pierre Rampal
2606      * update/change/correct ice age calculations
2607      * add age updates for pathological cases
2608      Probably needs more testing...
2609    
2610    checkpoint62x (2011/05/13)
2611    o pkg/mom_vecinv:
2612       high-order vorticity scheme: use interior masks (maskInW & S)
2613       to zero-out (outside OB) gradient of vorticity.
2614    o verification exp.:
2615       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
2616       hs94.128x64x5 and seaice_obcs ; update results.
2617    o pkg/obcs:
2618      fix bug in OBeta for YZ sections in obcs_exf_load.F
2619    o pkg/ctrl, pkg/shelfice, and optim:
2620      - add new control variable xx_shifwflx (fresh water flux underneath ice
2621        shelves). This is almost as tedious as obcs-ctrl, because the
2622        variables needs its own mask.
2623      - add a cost function term that penalizes the deviation of xx_shifwflx
2624        from the first guess (zero) in analogy to other control variables
2625    o pkg/shelfice:
2626      - start basic adjoint
2627    o pkg/ctrl:
2628      - remove extra 2D field "for good measure" when initializing in
2629        ctrl_set_globfld_[xy/xz/yz].F
2630      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
2631      - improve error messages in ctrl_set_unpack_*
2632    o OBC implementation in momentum:
2633       use interior masks (maskInC,W & S) in momentum S/R:
2634       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
2635       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
2636       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
2637       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
2638       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
2639        (and also with Leith/Smagorinsky harmonic-viscosity).
2640       Update output of experiment dome and exp4 (+nlfs).
2641    o exp4 test-exp:
2642      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
2643        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
2644        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
2645        time-varying OB at Western-side for wVel (NonHyd); update output.
2646      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
2647        and biharmonic-viscosity ; also use prescribed time varying OB.
2648    o pkg/obcs:
2649      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
2650    o model/src:
2651      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
2652      - initialise startTime & nIter0 with unlikely values: allows to set one
2653        from the other without ambiguity.
2654    o seaice_obcs test-exp.:
2655      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
2656    o pkg/obcs:
2657      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
2658        no longer needed with maskInC,W,S in pkg/generic_advdiff.
2659    o pkg/seaice:
2660      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
2661        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
2662      - fixed bug in the initialization of sea ice salinity variable HSALT
2663        in seaice_init_varia.F  (removed dependence on ICE2WATR)
2664    o fizhi-cs test exp.:
2665       switch reference output convention for these 2 non-standard test-exp,
2666        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
2667          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
2668       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
2669    o model/inc:
2670      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
2671        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
2672    o pkg/seaice:
2673      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
2674    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
2675      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
2676        and initial HSALT
2677    
2678    checkpoint62w (2011/04/26)
2679    o pkg/mom_fluxform:
2680      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
2681      - use parameter "sideDragFactor" in no-slip BC side-drag part.
2682      - update output of exp. global_ocean.90x40x15
2683    o pkg/mom_vecinv:
2684      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
2685    o update seaice exp.:
2686      use more consistent parameter values (remove "backward compatability only":
2687       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
2688      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
2689       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
2690    o update test-exp global_ocean.90x40x15:
2691      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
2692      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
2693      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
2694      o turn on zStar & viscA4 in standard set-up (dir input/)
2695        and update output files: output.txt & output.dwnslp.txt
2696    o new AD-test experiment: obcs_ctrl
2697      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
2698    o pkg/dic:
2699      fix two bugs in handling water vapour pressure in carbonate chemistry
2700      and air-sea fluxes. Found by Val Bennington and Galen McKinley
2701      (add DIC Option = WATERVAP_BUG to recover old results)
2702      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
2703    o adding allowInteriorFreezing option to check for water below freezing point
2704      at depth and bring the negative heat anomaly to the surface level
2705    o pkgs _fields_load:
2706      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
2707      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
2708        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
2709        rbcs to get interpolation weights and time reccord number.
2710      - fix multi-threading in aim_fields_load.F
2711      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
2712    o external_fields_load:
2713      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
2714       interpolation weights) to use in a periodic time-series ; do not divide by
2715       time-step to convert to integer:
2716       - this fixes case where externForcingPeriod is not multiple of time-step
2717          (Thanks to Christopher L. Wolfe)
2718       - this fixes case where externForcingPeriod is an odd multiple of time-step
2719         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
2720      store index of time-record which is currently loaded:
2721       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
2722       - needed for the adjoint but not yet used because of extensive recomputations;
2723         (to be fixed soon)
2724    
2725    checkpoint62v (2011/04/02)
2726    o verification/1D_ocean_ice_column added to test Ian Fenty's
2727      pkg/seaice_growth.F modifications for improving sea ice code differentiability
2728    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
2729      (new velocity statistics after changing maskInW & maskInS definition)
2730    o pkg/generic_advdiff with OBCS:
2731      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
2732      equivalent to assumption of no tracer gradient outside the OB region.
2733      This will affect the results if using obcs+biharmonic diffusion.
2734      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
2735    o pkg/obcs:
2736      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
2737      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
2738      in Interior region. No impact on solution but affects Velocity monitor stats.
2739    o pkg/ptracers (adjoint)
2740      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
2741      tape file for each tracer
2742    o model/inc/src and pkg/autodiff: add parameters that allow to turn
2743      of parts of the adjoint code at run time. For now, there are only
2744      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
2745      parameters are set in data.pkg.
2746      This is the lazy coward's version of doing this, but still useful for
2747      debugging. In order to do it right, everything needs to be moved to
2748      pkg/autodiff.
2749    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
2750      the end; this fixes the adjoint balancing code for open boundaries.
2751    o pkg/ctrl:
2752      - change behavior of xx_${varname}period to be analogous to exf-conventions:
2753        xx_${varname}period =   0.,  means time-independent control part
2754        xx_${varname}period = -12., means one-year-periodic monthly control part
2755      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
2756        clean up ctrl_init a little, remove unused variables
2757      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
2758      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
2759    
2760    checkpoint62u (2011/03/15)
2761    o model/src:
2762      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
2763        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
2764      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
2765        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
2766    o pkg/ctrl/obcs/ecco:
2767      - remove obsolete, unused, and partially broken code:
2768        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
2769        ALLOW_CTRL_OBCS_BALANCE
2770      - put a stop statement into ecco/cost_obcsvol.F, but also add
2771        cost_obcsvol to ecco_ad_diff.list
2772    o pkg/ecco: fix counting cost function contributions for obcs (code
2773      by Matt M.) and diffkr for diagnostics
2774    o pkg/ecco, pkg/ctrl, pkg/grdchk:
2775      add cost penalty terms for initial uvel, vvel, eta controls
2776      and I/O for prior error files
2777    o pkg/mdsio:
2778       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
2779       (new argument) to check for tiled file in mdsioLocalDir : this fix the
2780       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
2781    o pkg/ctrl:
2782     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
2783       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
2784       unused and superfluous variables
2785     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
2786    o pkg/ecco
2787     - enable adjoint of Stevens OB
2788    o pkg/ctrl/ecco/grdchk:
2789      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
2790        Fortunately, we do not have any tests for the numerous cpp-flagged
2791        option of "obcs as control parameters" so we will never know
2792        if this is an improvement (but at least now things compile).
2793      - remove an obsolete initialization from ecco_cost_init_barfiles.F
2794      - fix some problems within never used ifdefs to make the code compile
2795    o pkg/obcs:
2796     - Refine Interior mask definition to work with more complex OB (e.g.
2797       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
2798       read in Interior mask from file. Check if Interior mask is consistent
2799       with OB list of indices.
2800    o pkg/seaice
2801     - beginning code for a seaice tracer package,
2802       but currently only used for seaice age: SEAICE_AGE
2803       SEAICE_num = 4
2804       iTracer = 1: area-weighted ice age
2805               = 2: volume-weighted ice age
2806               = 3, 4: template for one-year vs. multi-year ice
2807       data.seaice has new namelist SEAICE_PARM03 for arrays related to
2808       SEAICE_num
2809    
2810    checkpoint62t (2011/03/05)
2811    o pkg/obcs:
2812     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
2813       then normal component. This ensures that the normal component is set
2814       correctly even when it conficts with tangential setting from an other OB.
2815       Affects results of test-experiment seaice_obcs: update the output.txt
2816    o pkg/obcs:
2817     - add code to monitor statistics of dynamical fields at OB.
2818     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
2819       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
2820       - change default: balance the Net inflow through all OB (instead of balancing
2821         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
2822     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
2823       to match Nortern OB inflow (OBCS_balanceFacN=0).
2824    o pkg/seaice:
2825     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
2826    o pkg/seaice (seaice_growth v 1.113):
2827     - reverting seaice_growth to v 1.111 in order to have code with exact bit
2828       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
2829       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
2830       runtime flag SEAICEareaFormula is kept but is inactive
2831    o model/src:
2832     - add new param to scale curvilinear grid distance and area when using
2833       a different sphere radius from the grid-files.
2834     - test/check multi-threads EXCH applied to local variable (cg2d_x)
2835    o adjoint:
2836     - enable adjoint of Stevens OB
2837     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
2838       (a bit delicate because of potentially modified adj. common block structure;
2839       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
2840    
2841    checkpoint62s (2011/02/15)
2842    o pkg/seaice (seaice_growth v 1.112):
2843     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
2844       computing the ice cover tendency from effective thickness tendencies. Include
2845       Ian Fenty's formula.
2846     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
2847       SEAICEareaFormula.
2848     - simplify notations for the various d_HEFF/d_AREA terms.
2849    o pkg/gmredi:
2850     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
2851       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
2852       add a verification test-run (front_relax.bvp) to test GM_useBVP.
2853    o pkg/seaice (seaice_growth v 1.111):
2854     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
2855     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
2856       also melt ice.
2857    o pkg/seaice:
2858     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
2859     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
2860    o pkg/cheapaml:
2861     - from Nico Wienders: New version of this package.
2862    o pkg/flt:
2863     - add CPP options to prevent floats to re-enter the opposite side of
2864       a periodic domain (default: keep periodicity)
2865    o pkg/gmredi:
2866     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
2867       (needed for multi-dim advection).
2868     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
2869    o model/src:
2870     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
2871    o tutorial_tracer_adjsens
2872     - extend to NLFS and replace maskC by hFacC
2873       (change reference output accordingly)
2874    
2875    checkpoint62r (2011/01/24)
2876    o testreport:
2877     - add option -deloutp (-do) to remove output file after successful run
2878     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
2879       extract exact list of procs from this file ; adjust COMMAND by
2880       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
2881    o pkg/ecco: replace old ineffective way of penalizing deviations from
2882      first guess (of obcs) with code by Matt Mazloff
2883    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
2884      exf/cal
2885      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
2886        and handle case of obcs?period == 0
2887        Not affected by these changes: There is still an inconsistency in
2888        the computation of start/endrec for the obcs variables for ALLOW_CAL
2889        defined (see comment by Menemenlis, 7-Mar-2003)
2890      - make S/R ctrl_get_gen_rec return something meaningful even if
2891        ALLOW_CAL is not defined
2892      - ctrl_getobcs?: simplify code so that it does not need to use
2893                       S/R exf_swapfields
2894    o testreport:
2895       allow to test MPI with different number of processors for each experiment:
2896       create file "SIZE.h.mpi" in each build dir.
2897       Note: update of "-command" argument not yet implemented.
2898    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
2899      alleviate the need for additional 3D tapes when using
2900      the non-inear free surface in the adjoint. This is done
2901      by adding an 'update' of hfacc etc. to their current
2902      value at the beginning of forward_step.F.
2903    o pkg/seaice
2904      seaice_lsr: move stress-divergence computations out of outer pseudo-
2905      timestepping loop
2906    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
2907      up, so that the calls of the ctrl_* subroutines are really at the end
2908      of the routine.
2909    o pkg/gmredi:
2910      allow to specify a 2-D horizontal map and a 1-D vertical profil
2911      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
2912    o pkg/seaice:
2913      move lsr iterations from seaice_dynsolver to seaice_lsr.
2914    o pkg/seaice:
2915      reduce memory footprint of seaice mutldim advection tapes,
2916      by using a 2D tape independent of the generic_advdiff ones,
2917      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
2918    
2919    checkpoint62q (2010/12/29)
2920    o model/src:
2921      - check horizontal grid-spacing for unset or zero/negative values.
2922      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
2923    o pkg/flt:
2924      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
2925      - precision of input and output files set according to readBinaryPrec
2926        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
2927      - initial float position from tiled file was not converted to index space
2928        (looks like a bug): fixed to make it similar to initial pos. global file.
2929    o global_ocean.cs32x15:
2930       change SIZE.h of AD set-up to get same tiling as with MPI.
2931       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
2932    o model/src:
2933       add flag to control printing of domain fields (bathymetry, hFac ...) in
2934       ini_mask_etc (call to plot_fieds_xy*).
2935    o pkg/thsice:
2936       if useEXF, some forcing fields are not valid in overlap: fixed by computing
2937       over the interior only + apply EXCH at the end (like with SEAICE advection).
2938    o pkg/mdsio:
2939      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
2940        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
2941      - change barrier call for safe multi-threads access to 3-D shared buffer.
2942      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
2943      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
2944        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
2945    o pkg/flt:
2946      - add fourth-order Runge-Kutta integration
2947      - add basic exch2 support (only 1 facet supported so far!)
2948    o pkg/mdsio+rw:
2949      new S/R to read local (or tile independent) vector (read counterpart of
2950       mds_writevec_loc, and front-end write_glvec_rl/rs).
2951    o global_ocean.cs32x15: additional input_ad.seaice experiment
2952        that uses pkg/seaice rather than pkg/thsice.
2953        (using multidim advection for seaice)
2954    o towards more F95 syntax for array specification in namelist:
2955      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
2956        of all verification experiments.
2957           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
2958          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
2959      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
2960    o global_ocean.cs32x15: additional input.seaice experiment
2961        that uses pkg/seaice rather than pkg/thsice.
2962    
2963    checkpoint62p (2010/12/17)
2964    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
2965        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
2966    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
2967        allow for use of multim. advection in seaice adjoint.
2968    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
2969      - first attempt to close budgets by taking into account the freshwater
2970        flux implied by the sublimation of snow and ice. So far only the
2971        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
2972        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
2973    o eesupp/src:
2974      new S/R with new option (NML_EXTENDED_F77) to change array specification
2975      from F95 standard to commonly accepted extended F77 form.
2976      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
2977      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
2978      for less tolerant f77 compiler (e.g., pgf77, g77).
2979    o globalFiles:
2980      commented out in parameter file "data" since it's not safe with MPI
2981      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
2982      in this case); no longer commented out in restart test (tst_2+2).
2983    o add adTapeDir to specify a special directory where adjoint tapes are
2984      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
2985      and cannot be used together with mdsioLocalDir.
2986    o nesting pkgs:
2987      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
2988      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
2989      - add parameter files + utils dir + output from short run on beagle.
2990    o pkg/seaice:
2991        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
2992    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
2993      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
2994    
2995    checkpoint62o (2010/11/25)
2996    o pkg/exf:
2997      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
2998    o pkg/seaice:
2999      - seaice_ocean_stress: split a loop for better vectorization of the
3000        adjoint code
3001      - seaice_growth.F: fix bug in conservation of freshwater connected to
3002        capping of heff, put contribution into d_HEFFbyNEG
3003      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
3004        by something more sensible (parameters that are what their name implies)
3005      - change some defaults, so that by default exf-parameters are used for
3006        things like rhoAir, cpAir,latent/sensible heat parameters, in order
3007        to reproduce the old results, many data.seaice now contain funny values
3008        for cpAir and latent heat of sublimation
3009    o packages_readparms.F: move exf_readparms up in line so that
3010        exf-parameters are visible for other packages (e.g. seaice)
3011    o debugMode & debugLevel=2:
3012      - differentiate between debugMode & debugLevel=2:
3013        debugMode: controls printing of debug messages (sequence of S/R calls).
3014        debugLevel: controls printing of algorithm intermediate results and stats.
3015      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
3016        => allows to print debug-stats without all sequence of call messages.
3017      - switch control of debug print from debugLevel to debugMode in many S/R.
3018    o pkg/obcs (obcs-sponge):
3019        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
3020        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
3021    o pkg/generic_advdiff:
3022      - record overlap minimum size for each advection scheme;
3023      - refine criteria on overlap minimum size;
3024      - check and stop (in gad_check) if overlap size is too small.
3025    o pkg/obcs:
3026      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
3027        once, in ptracers_implicit.F)
3028      - with seaice: remove test on empty file name in obcs_apply_seaice (always
3029        apply OB values when tile has OB)
3030    o model/src, coriolis setting:
3031      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
3032        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
3033        files (selectCoriMap=3) with any grid.
3034      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
3035    o pkg/seaice/seaice_growth.F:
3036        a few cosmetic changes that reduce the number of lines of code
3037    o pkg/obcs: add boundary conditions following Stevens (1990)
3038      - the code follows old MOM/NAOSIM code
3039      - so far it is only implemented for the eastern and western boundaries
3040        and NOT for pTracers
3041    o pkg/rbcs:
3042      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
3043        beginning of the first rbcs forcing period.
3044      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
3045        offline package, i.e., one file per time, labeled by iteration number;
3046        deltaTrbcs sets the timestep with which the data was generated;
3047        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
3048      - rbcsForcingCycle=0 makes forcing non-cyclic.
3049      - make arithmetic safe for negative times and odd forcing periods.
3050    
3051    checkpoint62n (2010/11/09)
3052    o pkg/seaice:
3053        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
3054    o pkg/obcs:
3055       New S/R to copy tracer value from the OB location to narrow band region
3056        (width = same as overlap) beyond the OB: preserve OB value (needed for
3057        high-order scheme) which were overwritten by EXCH call if in overlap
3058        region. Applied to theta, salt, ptracer and advected seaice variables.
3059       With seaice: use maskInC in similar way as in gad_advection.F,
3060        in seaice_advection.F and advect.F.
3061       Update output of experiment seaice_obcs and change exp4 to test OBCS with
3062        4th order Adv.Scheme. for pasive salt and ptracer.
3063    o tools/genmake2:
3064      - when looking for an optfile (not specified), only search for Fortran compiler
3065        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
3066      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
3067        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
3068      - set default for CPP to "cpp -traditional -P" (was the case without specifying
3069        an optfile, but otherwise default was just "cpp".
3070      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
3071      - when "CC" is not set in the optfile, look for possible C compiler
3072        (instead of just setting CC=cc)
3073      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
3074        => add a ".F" to ".o" rule for source files with no "#include" (such as
3075           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
3076      - move gfortran before g77 in list of possible Fortran compiler (consistent
3077        with reference compiler switch from g77 to gfortran)
3078    o pkg/seaice:
3079      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
3080        seaice_check that stops the model, when the CPP flag is used.
3081      o seaice_growth.F: make capping of ice volume conserving by returning the
3082        capped ice as freshwater to EmPmR. This does not change the verification
3083        experiments but will change runs where the capping is acutally active
3084    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
3085      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
3086         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
3087         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
3088    o tools/genmake2:
3089      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
3090      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
3091      - clean previous genmake log files before anything else.
3092      - change Makefile to remove testreport log files (*.tr_log) and genmake log
3093        files only with "CLEAN" target (instead of "Clean");
3094    o pkg/generic_advdiff:
3095      Change OBCS in multiDim advection (gad_advection.F):
3096       Use maskInC to prevent intermediate update of tracer-field in OB regions,
3097       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
3098       which were applying future time-step OB values.
3099      This way, all explicit calculations use current-time-step OB values
3100       (simpler and more consistent).
3101      Affects results when set-up uses time-varying OBC and multi-dim advection;
3102       update output of experiment seaice_obcs.
3103    o pkg/seaice:
3104      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
3105       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
3106         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
3107      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
3108       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
3109       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
3110    o pkg aim (2010/10/26):
3111      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
3112        formulation with obliquity, eccentricity, ... as run-time parameters,
3113      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
3114        upward shortwave radition at the surface (all-sky and clear-sky).
3115    o pkg/obcs:
3116      - writing sections with globalFiles=T does not work: switch to tiled-files
3117        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
3118      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
3119      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
3120    
3121    checkpoint62m (2010/10/21)
3122    o pkg/seaice: vectorize seaice_solve4temp.F
3123      - move iterations loops outside of i/j-loops
3124      - requires 2D arrays for TB and effConduct
3125      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
3126        modified in this routine
3127      - a little bit of clean up, adjusting indentation, etc.
3128      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
3129        performance and '**TWO' by '**2' (because TWO is a float),
3130        replaced ONE, ZERO
3131    o eesupp/src:
3132       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
3133    o pkg/seaice/seaice_growth.F
3134      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
3135      merging process. The merged routine has two branches, and one activates the 'evolution'
3136      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
3137      In summary, here is what the '10/10 revision' did consist of
3138        part 1: seaice_growth.F revisions 1.71 to 1.75
3139          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
3140            The emphasis here was on improving readability (e.g. by trying to use meaningful
3141            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
3142        part 1.5:
3143          - revising the lab_sea experiment to make it a more useful (i.e. stable
3144            and representative of an actual model run). This was done by generating a
3145            (winter) pickup to start from, switching back the main experiment dynamic
3146            solver from evp to lsr, having one of the experiments use the free drift solution.
3147        part 2: seaice_growth.F revisions 1.76 to 1.85
3148          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
3149          - Sorting out the various fields units and sign (set early on and reset at the end)
3150            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
3151            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
3152          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
3153            and simplifying logical expressions to further improve readibility.
3154        part 3: seaice_growth.F revisions 1.86 to 1.89
3155          - Re-organize the blocks of code more logically.
3156          - Merging the '_if.F' pieces that add something new.
3157    o pkg/thsice:
3158      - vectorize thsice_solve4temp and thsice_get_exf.
3159        Problem: thsice_solve4temp has an unvectorizable statement that
3160        might also be problematic for TAF
3161      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
3162        does not change the verifcation experiment, but will change all
3163        experiments that have this flag undefined (not tested in verification);
3164        a little reorganization to save a few 2D fields and recomputations
3165      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
3166      - 2nd step:  fix some store dirs
3167        o seems to work somewhat, i.e. using ifort but not g77
3168        o likely cause are incomplete init. or recomputation
3169        o start verification/global_ocean.cs32x15/input_ad.thsice
3170    o pkg/obcs: add support for exch2
3171      - the position of the boundary and prescribed values are specified using
3172        a global domain with exch2 facets stacked
3173        - in x for N,S boundaries (like W2_mapIO=-1)
3174        - in y for E,W boundaries (so E,W boundaries do not overlap)
3175    o pkg/mdsio: add support for writing global sections with exch2
3176        file layout is as for obcs described above:
3177        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
3178        - for y-z sections, facets are stacked in y
3179    o pkg/thsice:
3180       - change a few routines for better vectorization: thsice_albedo.F,
3181         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
3182         not affected, but in particular the latter routine has changed
3183         dramatically (not necessarily easier to read now).
3184       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
3185       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
3186    o verification/lab_sea:
3187      - overhaul of the forward model experiments. The main motivation
3188        for this revision is that lab_sea has proven quite fragile (when
3189        changing the sea-ice code, and switching platforms) to a point
3190        when failures were very hard to attribute to specific code problems.
3191      - the suspected reason for this fragility is noise amplification by evp so,
3192        to start with, we decided to replace evp with lsr in the main experiment.
3193      - the input.lsr experiment thus became obsolete and was removed.
3194      - it was replaced with the input.fd experiment that uses an
3195        analytical "free drift" solution as the ice velocity field.
3196      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
3197        will hopefully allow us to discriminate problems due to dynamic solvers
3198        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
3199        us to test additional options, along with the salt plume package.
3200      - Finally a pickup was generated (at the end of a one year run) to
3201        make the tests more representative of an actual model run. Previously
3202        the tests starting point was a 1m thickness of ice everywhere.
3203    o pkg/seaice:
3204      - introducing S\R seaice_freedrift.F that compute the
3205        analytical solution to an approximate ice momentum
3206        equation (i.e. the simple stress/coriolis balance).
3207      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
3208        of the free drift velocity field, and enable its use.
3209        To actually use the free drift solution as the model ice
3210        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
3211    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
3212    
3213    checkpoint62l (2010/10/04)
3214    o pkg/seaice:
3215      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
3216      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
3217       version (with USE_ORIGINAL_SBI undef);
3218    o add hooks for new packages OASIS, the package will follow
3219      (hooks exclude the seaice pkg for now)
3220    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
3221      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
3222      rather than mdsio_readvector.F/mdsio_writevector.F, within
3223      adread_adwrite.F to read/write adjoint-related tapes to disk.
3224    o eesupp and pkg/mdsio: ALLOW_WHIO
3225      Option to write/read 2D fields to files including tiles halos.
3226      The main purpose is for adjoint related "tape I/O".
3227      The secondary purpose is for debugging phases.
3228      A word on those rather specifically intended purposes.
3229      The code was meant to be stripped down to the bare minimum.
3230      Typically, there is a unique and basic mapping to the global
3231      buffer (tile by tile, then proc by proc, then level by level), and
3232      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
3233      meant to generate user friendly outputs of various shapes and forms.
3234      Rather it is intended, for the knowledgeabale developers,
3235      to be largely independent of the many mdsio options, to allow
3236      outputs of tiles+halos in debugging phases and in adjoint runs,
3237      and to allow some flexibility in tuning (adoint) I/O depending on each
3238      file system behavior. With regard to tuning, most of the potential knobs
3239      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
3240      to specify directories, to specify the typical size of I/O calls, etc.)
3241      are not yet included, and will be added if they prove useful.
3242    o pkg/seaice:
3243       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
3244    o pkg/seaice:
3245       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
3246       code (seaice_budget_ice_if.F) which enable to recover old standard
3247       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
3248       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
3249    o model/src (rStar):
3250       use simple average (not area weighted) of rStarFac at U,V point when using
3251       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
3252       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
3253    
3254    checkpoint62k (2010/09/17)
3255    o adjoint
3256       * changed verification/global_ocean.cs32x15 ; adjoint now tests
3257         Adams-Bashforth 3 + NLFS + RSTAR
3258       * some more modifs required for ECCO-GODAE v4
3259    o pkg/seaice
3260       add SEAICE_AGE_VOL option to use volume instead of area for
3261       integrating SEAICE_AGE
3262    o model/src:
3263       first check-in of sigma & hybrid-sigma coordinate code ; also includes
3264       non-linear free-surface parts ; but pressure-gradient not yet coded.
3265    o pkg/ptracers:
3266       option for ptracer to convert Salt Relax into additional EmP.
3267        tested in exp. global_ocean.90x40x15.dwnslp (update output)
3268    
3269    checkpoint62j (2010/08/25)
3270    o pkg/ggl90:
3271       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
3272    o pkg/dic: car_flux.F, phos_flux.F
3273      - reduce number of exp-calls in order to improve performance
3274      - clean up a little (replace fields by their macros, etc., fix
3275        typo in CPP-flag)
3276    o pkg/ggl90: minor changes
3277      - GGL90diffKrS was removed --> always use GGL90diffKr
3278      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
3279      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
3280        (commented out for now)
3281      - change in max/min operations to ensure that smoothing is ok
3282      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
3283      - always use diffKrNrT as background profile (i.e. never use diffKr field)
3284    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
3285    o pkg/dic:
3286      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
3287        vectorization
3288      - small bug fix in insol for the unlikely case of a cartesian grid
3289      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
3290        + now vectorize, which also removes adjoint recomputations;
3291        + replace integer maksp1 by _RL maskp1
3292        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
3293    
3294    checkpoint62i (2010/07/21)
3295    o pkg/flt:
3296      - with OBCS: stop floats which enter the OB region
3297    o model/src:
3298      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
3299        for implicit vertical advection.
3300    o pkg/seaice:
3301     - account for melting in seaice age evolution.
3302     - remove double counting of seaice ridging effect on seaice age.
3303    
3304    checkpoint62h (2010/06/18)
3305    o pkg/exch2:
3306     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
3307    o tools/genmake2
3308      - remove "-pdefault" option: redundant with the use of "packages.conf";
3309      - remove file pkg/pkg_default : set the default as a pkg group
3310        ("default_pkg_list") defined in pkg/pkg_groups;
3311      - fix for case pkg/pkg_depend is missing (was hanging before);
3312      - add option "-pgroups" to specify a different pkg_groups than the default.
3313    o verification/adjustment.cs-32x32x1:
3314       add a "minimal" set-up test (code_min & input_min) which only compiles
3315       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
3316    o tools/genmake2
3317      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
3318      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
3319    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
3320      files are nearly the same anyway.
3321      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
3322       - redefinition of tau(i,i) (by a factor of ustar)
3323       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
3324       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
3325       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
3326       - replace
3327         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
3328         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
3329         by
3330         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
3331         (changes results)
3332       -> exf_bulkformulae v1.22,
3333          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
3334          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
3335                    output.txt 1.63
3336           offline_exf_seaice: output.seaicetd.txt 1.7
3337           seaice_obcs: output.txt 1.10)
3338      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
3339       -> exf_bulkformulae v1.23,
3340          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
3341          and global_ocean.cs32x15.icedyn (only 11 matching digits)
3342      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
3343    o adjoint of exch-1:
3344     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
3345       (note: was already like this when using EXCH-2) and remove flow dir
3346       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
3347     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
3348     - update pkg/exch2 diff list.
3349    
3350    checkpoint62g (2010/05/19)
3351    o eesupp/src (exch-1):
3352     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
3353       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
3354       (renamed to exch1_*rx_cube.F).
3355     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
3356       to call new exch1 S/R ; update Makefile and .cvsignore.
3357     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
3358       exch2_xy_rx later)
3359      Note: after updating your code, need to run "make clean" in eesupp/src
3360    o test experiment bottom_ctrl_5x5:
3361       new output_adm.txt with fewer grdchk & less monitor output.
3362    o model/src:
3363      remove the call to ini_cori in initialise_varia.F (just keep the usual one
3364       in initialise_fixed.F). More consistent with coriolis & horizontal grid
3365       beeing treated in the same way (ini_grid is not called a 2nd time).
3366    o pkg/exf:
3367      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
3368      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
3369      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
3370      - cosmetic changes to exf_bulkformulae.F to make it look more like
3371        exf_bulk_largeyeager04.F
3372    o eesupp/src (exch-1):
3373      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
3374      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
3375        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
3376        (even without using MPI).
3377      - Message mode: move RecvAck setting (indicator of buffer being ready)
3378        from send_put to recv_get S/R (was useless before, but not sure if
3379        it's much more useful now);
3380      - Switch the order of sync: MPI-proc 1rst and then threads;
3381      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
3382      - fix AD code for communication mode ='get' (but not used).
3383    o model/src:
3384      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
3385      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
3386    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
3387    o pkg/ctrl: require a specific set of control variables and exf-flags for
3388      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
3389    o model/src:
3390     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
3391       1rst forward sweep, to avoid over-writing output files during recomputations
3392       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
3393     b) 2nd version:
3394      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
3395      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
3396         writePickupAtEnd) + seaice & ptracers output;
3397      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
3398    o model/src:
3399      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
3400    o pkg/exch2:
3401      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
3402      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
3403    o pkg/autodiff & exch2:
3404      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
3405      (for now, only if ALLOW_EXCH2 is defined).
3406    o pkg/autodiff:
3407      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
3408        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
3409       + clean-up comments (_RS is not always real*4)
3410      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
3411      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
3412        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
3413    o testreport (AD-tests):
3414      no longer link files from dir "../input" (1rst link files from
3415      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
3416    
3417    checkpoint62f (2010/04/29)
3418    o model/src/the_main_loop.F:
3419      adjust store directives for seaice evp and multicategory according to
3420      pkg/ecco/the_main_loop.F
3421    o adjoint:
3422      global_sum_ad was incomplete (noted many times by many people ;)
3423      nice description by Jean U. as follows:
3424      * allreduce(var) in global_sum.F can be interpreted as
3425        reduce(sum) followed by broadcast of sum.
3426      * The adjoint of that is
3427        sum(adjoint) followed by broadcast(summed adjoint value)
3428        or in other words, allreduce(sum, adjoint vars)
3429      We were missing the sum(adjoint)!
3430      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
3431      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
3432      The fix should produce 16-digit accuracy between
3433      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
3434      multi-CPU single-tile (e.g. nSx=1, nPx-2)
3435      We'll probably change this yet again shortly
3436    o eesupp/src:
3437      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
3438    o pkg/icefront
3439      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
3440        specification of addmass array based on a 2D field, which is added
3441        at bottommost wet level at each horizontal location.
3442    o model/src:
3443     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
3444     layout; (not always compatible with delX,delY setting; commented out for now).
3445    o pkg/exch2:
3446     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
3447     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
3448    
3449    checkpoint62e (2010/04/15)
3450    o pkg/obcs:
3451      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
3452    o pkg/dic:
3453      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
3454        (note: not presently tested in any forward verification exp.)
3455       update tutorial_global_oce_biogeo AD output file.
3456    o pkg/exf:
3457      - account for the variation of albedo as a function of zenith angle
3458        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
3459    o build_options:
3460     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
3461    o pkg/dic:
3462      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
3463      - use binary pickup file for restart;
3464      - initialise atmos-CO2 box from dic_pCO2 parameter;
3465      - fix multi-threaded.
3466    o pkg/rbcs:
3467     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
3468       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
3469     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
3470       and update output.txt
3471    o pkg/kpp:
3472     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
3473     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
3474       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
3475       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
3476     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
3477       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
3478    o pkg/offline:
3479      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
3480      (bug was added in version 1.10 on 2007-08-23).
3481    o pkg/offline:
3482      - no need to specify periodicExternalForcing, etc ... to use offline pack
3483      - offline input files no longer just single prec --> parameter offlineLoadPrec
3484    o verification/lab_sea:
3485      change AD test to multi-tile setup and update all 4 AD output.
3486      NOTE: while cost function values remain very similar,
3487      gradients are very different, although gradient checks are self-consistent
3488      Should try to get to the bottom of this (cost function summation order?)
3489    o pkg/dic:
3490      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
3491      a weakness of TAF that drops part of double precision in log10 derivative.
3492      <= changes removed since problem has been fixed in current TAF version 1.9.71
3493      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
3494    o pkg/ecco:
3495      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
3496      update all 4 lab_sea AD output.
3497    
3498    checkpoint62d (2010/03/22)
3499    o build_options:
3500      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
3501    o remove unbalanced quote (single or double) in commented line of source code
3502      (may cause some warning with some preprocessor/makedepend versions).
3503    o pkg/seaice:
3504      fix seaice_model.F for adjoint (gael) and update AD results of experiments
3505       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
3506    o testreport:
3507      add option '-runonly' (short: '-ro') to just do the run part (without make).
3508    o eesupp: remove JAM communication code (obsolete).
3509    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
3510      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
3511      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
3512      (update also the output).
3513    
3514    checkpoint62c (2010/03/02)
3515    o tools/build_options :
3516       move (some) old optfiles from build_options/ to build_options/unsupported/
3517    o model/src and pkg/exf
3518       surface relaxation -- separating data and data.exf options
3519       The point is to ensure that we specify the surface relaxation
3520       either in data or in data.exf (but not half and half) and to
3521       avoid an accidental relaxation to 0 (which happened if a time
3522       scale was specified but the file name was left empty)
3523    o model/src model/inc and pkg/mom_common
3524       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
3525       => addition to the viscosity field as computed by others schemes
3526    o tools/build_options:
3527      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
3528        but keep the former optfile for few weeks for smooth transition
3529    o pkg/ecco
3530      - allow user defined cost function contributions
3531         CPP: ALLOW_USERCOST_CONTRIBUTION
3532         USAGE: compute contributions in cost_usercost_all.F
3533      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
3534          the two options are complementary.
3535    o pkg/smooth
3536      - migration from contrib to the main repository
3537    
3538    checkpoint62b (2010/01/26)
3539    o pkg/monitor:
3540      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
3541        (in case someone forgot to update customized pieces of code)
3542    o nonHydrostatic:
3543      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
3544      - add a simple 2-D experiment (short_surf_wave) to test it.
3545    o pkg/icefront:
3546       adding the shell of, and the hooks to, a new package that
3547       will model melting and freezing of vertical glacier ice fronts
3548    o momentum:
3549      add diagnostics of momentum tendency from Hydrostatic pressure gradient
3550       (without surf.pressure term: would need a 2nd filling since implicit term).
3551    o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
3552      two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
3553      cannot deal with the former
3554    o cleaning:
3555      - remove all (except OpenAD) old TLM output from results_ad dirs.
3556      - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
3557      - comment out maskH definition (replaced by maskInC)
3558    o pkg/monitor:
3559      - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
3560        & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
3561    
3562    checkpoint62a (2010/01/15)
3563    o model/src:
3564      - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
3565    o pkg/diagnostics:
3566      - add optional level number diagnostics (i.e., level number to be define
3567        explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
3568      - strictly check for valid parser-code(10) ;
3569      - check if adding diag to the list from the right place.
3570    o pkg/longstep:
3571      - change parameters and fix tracer conservation with rstar/nonlinear free surface
3572    o diagnostics:
3573     - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
3574       S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
3575    o pkg/diagnostics:
3576     - Add option for writing vertical integral (sum of selected levels) of an output
3577        field instead of writing output field levels. Activate this option on a per
3578        output-file basis, by setting the 2nd character of fileflag to 'I'.
3579     - Add field-specific information relative to level integral in 3rd postion
3580        of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
3581        vertically (x level-thickness x hFac), "r"=same but without hFac.
3582    o do_the_model_io:
3583      - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
3584        in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
3585        writing pickups and stopping.
3586    o pkg/diagnostics (for now, only with mdsio):
3587      - write time information to meta file (and modify accordingly rdmds.m) :
3588        time-averaged diagnostics output: write starting and ending time of the
3589        time-averaging interval ; snap-shot diagnostics output remains unchanged;
3590    o pkg/timeave:
3591      - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
3592        always Nr), now assumed to be equal to number of levels of averaged field;
3593        only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
3594    o pkg/sbo:
3595      - fix ocean bottom pressure global-average & 2-D time-ave output (was
3596        neither initialised nor filled).
3597      - add starting iteration in suffix of global-average output file
3598        (to avoid over-writing the file after a restart)
3599      - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
3600    o time-average:
3601      - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
3602        (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
3603         ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
3604        this fix DIC_COST cumulative-time array (previously: bi,bj,k)
3605      - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
3606      - fix missing accumulation for pkg/opps.
3607      - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
3608         (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
3609      - fix initialisation of time-ave vars and do only full time-step increment
3610        (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
3611    o pkg/layers:
3612      - use standard RW pkg S/R to write the output
3613        and remove local write_fld version (which had a problem).
3614      - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
3615      - fix LAYERS_CALC argument list.
3616    o pkg/timeave:
3617      - store cumulative-time in a simple tiled array (drop the level index)
3618      - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
3619    o pkg/ocn,aim_compon_interf
3620      - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
3621    
3622    checkpoint62  (2009/12/23)
3623    o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
3624        (was not previously tested in any other exp.)
3625    o pkg/monitor:
3626      - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
3627        mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
3628        (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
3629      - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
3630      - change del2 calculation.
3631      - use interior masks (instead of maskH, <- to be remove).
3632      - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
3633    o mask & obcs:
3634      - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
3635      - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
3636        (called after packages_init_fixed)
3637    o pkg/obcs:
3638      - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
3639        Fixes bug in obcs+exf with nSx*nSy.GT.1
3640      - fix multi-tile handling in obcs balance code
3641    o nonHydrostatic:
3642      - Implement AB-3 for non-hydrostatic vertical momentum ;
3643        (change ordering of var. stored in pickup file when using NH)
3644      - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
3645      - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
3646        (in prep. for new NH free surface form).
3647    o pkg/obcs:
3648      add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
3649    o model/src:
3650      fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
3651    
3652    checkpoint61z (2009/12/01)
3653    o nonHydrostatic:
3654      Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
3655        a spurious source of energy in simple baroclinic adjusment test case.
3656      Update all non-hydrostatic exp output.
3657    o model/src (3-d solver):
3658      Change again 3-D solver free-surface RHS term when exactConserv=T:
3659        simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
3660        (which was not the case with previous formulation).
3661      To recover previous version, just reset "oldFreeSurfTerm" to previous value.
3662      Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
3663    o nonHydrostatic:
3664      - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
3665        for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
3666      - change 3-D solver to work with r* (for now, only with linear free-surf.)
3667      - add few debug diagnostics (cg3d_x, residual)
3668    o model/src:
3669      fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
3670        update output of exp. global_ocean.cs32x15.viscA4
3671    o update output of exp. global_ocean.cs32x15.icedyn after removing
3672      #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
3673    o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
3674    o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
3675      for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
3676    o model: add Christopher Wolfe's implemetation of the single reduction cg2d
3677      (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
3678      runtime flag useSRCGSolver. Modify verification experiment global_with_exf
3679      to test this code
3680    o pkg/cd_code:
3681      Change defaut D-grid time-stepping to get the same for D-grid momentum as for
3682       C-grid momentum. D-grid velocity used to be stepped forward in time with
3683       Adams-Bashforth only on surface pressure term. Tests show that using AB on
3684       D-grid coriolis term improves stability (as expected from CD-scheme paper).
3685      To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
3686      Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
3687       lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
3688       tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
3689      Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
3690           global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
3691    o pkg/obcs:
3692     - fix bug in initialisation (broken since Oct 1rst modification)
3693       for useOBCSprescribe without useEXF.
3694    
3695    checkpoint61y (2009/11/15)
3696    o pkg/seaice
3697     - change (once again) the discretization for the evp solver: rather than
3698       squaring the averages of strain rates, average the squares to give
3699       a better approximation to VP behavior (in simple test); this breaks
3700       verification experiments that use EVP (lab_sea and lab_sea.hb87)
3701        --> update outputs
3702    o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
3703      to improve vectorization of adjoint code on TARGET_NEC_SX
3704    o verification/vermix:
3705      - change vermix to a more "classical" 1d column with high vertical
3706        resolution, seasonal heat flux forcing and constant wind forcing
3707        --> update outputs
3708    o pkg/seaice
3709     - fix diagnostics of principal stress components for EVP
3710     - add optional diagnostics of non-linear convergence for LSOR solver
3711     - make maximum zeta a runtime parameter
3712    o model/src (3-d solver):
3713      Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
3714       which consisted in removing the Surf. Non-Hydrostatic pressure from the
3715       whole column and adding it to Eta (inspired from Casualli, 1999):
3716       Only affects 3-D solver initial guess and only if using ExactConserv,
3717       but tests did show a degradation of solver convergence. For this reason,
3718       decide to disable this piece of code.
3719       to recover previous version, just set zeroPsNH = exactConserv (line 78).
3720      Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
3721    o pkg/ggl90:
3722     - fix previous modif (unfortunatly has not been documented here).
3723    o pkg/seaice/autodiff:
3724     - add CPP flag to include clipping of zeta in EVP code;
3725       although clipping of zeta is not necessary for EVP and not recommended
3726       it was done by default, now clipping is disabled by default
3727     - modify computation and store zetaC/Z in seaice_evp for TAF
3728     - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
3729     - change seaice_calc_viscosities/strainrates for better
3730       vectorization after AD by TAF
3731     - rearrange common blocks in SEAICE.h once again for easier dumps of
3732       adjoint output, adjust adcommon.h and g_common.h
3733     - change flux form of default advection scheme for better vectorization
3734       of adjoint code
3735     - modify lab_sea/input.lsr to test the flux form of default advection
3736       scheme
3737    o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
3738      transition in checkpoint61r)
3739    
3740    checkpoint61x (2009/10/19)
3741    o adjoint: adding two new verification experiments
3742      * tutorial_global_biogeo: an online dic sensitivity experiment
3743        (work with G. Forget)
3744      * tutorial_dic_adjoffline: an offline dic sensitivity experiment
3745        (an update of the Dutkiewicz et al., 2006 paper)
3746      Both use the same CO2FLUX cost function, but different controls
3747      Gradient checks look good, but some recomp. could still be traightened out
3748      Should add xx_dic control variable to test at some point
3749    o model/src:
3750      add run-time parameters to check and/or mask initial Temp & Salt
3751    o pkg/ptracers:
3752      apply zonal filter (if used) to all passive tracers
3753    
3754    checkpoint61w (2009/10/12)
3755    o adjoint:
3756      * update and finish work on adjoint of dic package (G. Forget)
3757      * start adjoint of offline package
3758      * bug fix for cube-sphere TLM code (active_file_g.F)
3759    o tutorial_global_oce_optim:
3760      now tested with 4 tiles (change data.grdchk and update output_adm.txt)
3761      and add SIZE.h_mpi for MPI testing
3762    o pkg autodiff
3763     - fix bug in autodiff_restore
3764     - make genmake2 remove comments and empty lines from ad_input_code.f in
3765       order to reduce file size (new script file remove_comments_sed)
3766    o allows to specify vertical profile of vertical viscosity (viscArNr)
3767    o pkg autodiff
3768      autodiff_ini_model_io: comment out writing of grid information to netcdf
3769      files, because at this time the grid fields are a bunch of zeros
3770      (this is analogous to ini_mnc_vars.F)
3771    o pkg seaice/autodiff:
3772     left-over from removing the 3-time-level fields:
3773     - small rearrangement of common blocks (SEAICE.h)
3774     - fix field declaration in order to get meaningful output in
3775       adseaice.*.nc (adcommon.h)
3776    o pkg obcs:
3777     - go through NH code only if nonHydrostatic=T
3778     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
3779     - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
3780       => Update output of experiment seaice_obcs
3781     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
3782     - fix NH+Orlanski restart (add wvel OBC value in pickup file)
3783     - fix restart for useOBCSprescribe + useEXF
3784    o pkg ctrl
3785     - make obcs as control parameter work also with useSingleCPUio
3786     - replace a few sny and snx by Ny and Nx to be consistent with
3787       ctrl_set_globfld_x/yz.F
3788    o pkg seaice
3789     - re-introduce global field frWtrAtm for the case of
3790       ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
3791     - catch the case of an empty filename in seaice_cost_init_fixed.F
3792    o pkg ecco:
3793     - small bug fixes in the_main_loop
3794      . fix order of monitor arguments
3795      . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
3796      . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
3797        that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
3798     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
3799       imbalance diagnostics for wmean_h/sflux = 0
3800     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
3801     - catch the case of empty filenames in ecco_cost_init_fixed.F
3802       and ecco_readparms.F
3803     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
3804       to make this statement meaningfull in ecco_cost_weights.F
3805    o pkg zonal_filt:
3806      - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
3807      - when using rStar, filter uVel*hFacW instead of uVel
3808       (tested without topography: fix a Pb of growing instability with NLFS)
3809    o pkg/aim/thsice:
3810     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
3811      (works as SST restoring)
3812    o pkg/thsice:
3813     -add specific parameter for salt restoring in slab mixed-layer
3814       (by default equal to the temperature restoring)
3815    
3816    checkpoint61v (2009/09/21)
3817    o pkg/kpp:
3818     -add double diffusive contributions as a hack, turned off by default
3819      for now, and the code can be excluded with a CPP-flag
3820      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
3821     -add a verification experiments to "vermix" to test this code
3822    o pkg/mom_common:
3823      Move computation of length scales to mom_init_fixed.F (avoid recomputation
3824      at each time-steps*levels).
3825    o pkg/layers:
3826      Created a new package for computing volume fluxes in temperature or
3827      [not yet implemented] density layers, e.g. for calculating residual
3828      overturning circulations.
3829    o pkg/diagnostics:
3830      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
3831    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
3832    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
3833      To avoid mixing type (RS/RL) of input/output array argument,
3834      replace single mixed-type array with a pair from each type (RS/RL).
3835    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
3836      is now implemented for all pkgs (previously only done for the main pickup)
3837    
3838    checkpoint61u (2009/08/25)
3839    o pkg/obcs:
3840      - change OB?eta from _RS to _RL and put them into a separate commen block
3841      - add code to read OB?eta from a file via obcs_prescribe_read: the code
3842        compiles and does not destroy any other experiments, the data is read
3843        properly, but the code is not tested in actual applications
3844    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
3845      create a meaningful unit attribute for the time coordinate variable
3846    o pkg/ebm: add plenty of missing "_d 0" ;
3847       update results of experiment global_ocean_ebm (fwd + adjoint tests)
3848      Notes: several pieces of code only works for (very) specific set up
3849       (domain size, lat range, etc ...); should be documented & stop if one
3850       of those assumptions is not meet.
3851    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
3852       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
3853          and offline_exf_seaice (seaicetd + adjoint).
3854    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
3855       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
3856        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
3857    o few changes to pass when compiling with strick checking of arguments
3858       across S/R (allow to find few bugs in S/R calls).
3859    o pkg/seaice:
3860     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
3861       2d-fields, for slightly better performance
3862    
3863    checkpoint61t (2009/07/22)
3864    o pkg/seaice:
3865     - remove unused variables in seaice_evp
3866     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
3867    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
3868       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
3869       each processor opens a different file (a fix from Matt).
3870    o cg2d:
3871       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
3872       this reduces number of EXCH calls by 2 when using exch2.
3873       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
3874       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
3875    o pkg/thsice:
3876       add code for Near Infra-Red albedo (from Jeff)
3877       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
3878    o ini_model_io:
3879       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
3880       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
3881       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
3882    
3883    checkpoint61s (2009/06/30)
3884    o pkg/exch2 (exch2_rxN_cube*):
3885       remove last BARRIER (no need to synchronise after getting data from shared
3886       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
3887    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
3888      and generate new output (for the 2 tests) using default rotationPeriod.
3889    o pkg/exch2:
3890      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
3891        (was already the case with AUTODIFF_EXCH2 defined)
3892      - add bj in exch2 arrays and S/R.
3893      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
3894        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
3895    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
3896      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
3897        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
3898      - verification experiment natl_box.longstep
3899    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
3900      allow different versions of ifort (8 or 9) and different versions
3901       of mpi (mpich or mpich2) to be used with the same optfile.
3902      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
3903       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
3904    o pkg/seaice:
3905      fix previous modif (3-level field removed) for old-pickup reading
3906    
3907    checkpoint61r (2009/06/25)
3908    o pkg/seaice:
3909     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
3910      1. introduce fields for time step (N-1)
3911      2. do not use levels 2 and 3 anymore (but keep them)
3912      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
3913         includes changes to pkg/thsice/thsice_get_velocity.F,
3914         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
3915         pkg/obcs/obcs_apply_uvice.F.
3916     - completely remove code for leap-frog time stepping for second order
3917       advection
3918     - adjusted adjoint accordingly;
3919       gradient checks have improved by an order of magnitude!
3920    
3921    checkpoint61q (2009/06/22)
3922    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
3923     - the boundary conditions along open boundaries are unclear, because the
3924       associated masks are set to zero and are thus treated as closed when
3925       applying the slip-boundary conditions.
3926     - move initialisation of grid variables from seaice_init_varia to _fixed
3927    o adding doc/diags_changes.txt
3928    o model/src:
3929      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
3930       to avoid "_diags" naming if no relation to pkg/diagnostics.
3931      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
3932       file and only call PLOT_FIELD_XYZ if debugMode=T.
3933      remove few PLOT_FIELD_XY calls outside initialisation.
3934      remove few unnecessary BARRIER.
3935    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
3936      of salt_plume package in Southern Ocean
3937    o pkg/thsice:
3938     - fix hOceMxL in overlap (needed for sea-ice advection);
3939       update output of experiment global_ocean.cs32x15.icedyn.
3940    o pkg/seaice:
3941     - make the (placeholder-)tracer IceAge a little more meaningful
3942      by avoiding ridging of age due to convergent ice flow
3943     - add diagnostics for surface temperature, atmospheric and oceanic
3944       heat flux, and atmospheric and oceanic ice growth
3945    
3946    checkpoint61p (2009/06/10)
3947    o eesupp (global_max & global_sum):
3948     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
3949     - remove starting & endding barrier (no longer needed)
3950    o pkg/mdsio, writelocal:
3951       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
3952       (remove the STOP): uses shared buffer IO to store data from all threads
3953       and then let master-thread write nThreads tiles.
3954    o pkg/mdsio (read/write field):
3955     - tiled IO done in 1 piece (all levels at a time);
3956     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
3957     - multi-threaded: allow to read/write local (non-shared) array
3958       (was already working with singleCpuIO ; now works also without);
3959       => no longer needs barrier call after reading a file (added inside
3960       mds_read/write field).
3961     - move barrier calls outside gather/scatter_2d to mds_read/write_field
3962    o pkg/obcs/exf
3963      - exf_getffieldrec.F: add a few ". _d 0" and
3964                            add code to catch the case fldperiod = 0.  
3965      - obcs_precribe_read.F: change if statements so that they match
3966                              the variable type (_RL)
3967      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
3968        exf_iprec) as part of namelist EXF_NML_01
3969    o pkg/mdsio:
3970      - read/write tiled (local) files: read/write 1-level tile chunk at a time
3971        (instead of segment of length sNx); expected to speed up tiled IO.
3972    o pkg/exch2:
3973      - take buffer copy from/to array out of S/R exch2_send/recv into new
3974        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
3975        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
3976      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
3977      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
3978        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
3979        including Topology header file (and common blocks).
3980      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
3981        remove 2nd exch call in exch2_s3d_rx (no longer needed).
3982      - document S/R arg. list (+ update some comments)
3983    o pkg/seaice:
3984      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
3985        temperature and humidity over sea ice based on climatological values.
3986      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
3987        of LSR (this change is expected to change the results slightly because now
3988        it uses slightly difference moduli from the second last LSR solution, but
3989        that is more consistent with the stress computations; this part of the code
3990        is not tested in the verification experiments)
3991      - fix diagnostics for flux of ice in case of B-grid
3992      - turn strain rates eij and press into global fields within global
3993        common block in SEAICE.h for more straighforward diagnostics
3994      - fix diagnostics for principal stress components, press, zeta, eta
3995        to give something meaning full
3996    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
3997      new output (all 4 tests) using default rotationPeriod.
3998    o pkg KPP:
3999      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
4000      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
4001        and normal grid from 1 to Nr)
4002    o Fix computations of L4rdt in mom_calc_visc.F
4003    o eesupp:
4004      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
4005      should be called before a "stop" if we know that all process are going
4006      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
4007    
4008    checkpoint61o (2009/05/26)
4009    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
4010    o model/src/ini_curvilinear_grid.F:
4011       compute angleSin/CosC when they are not read from a file
4012    o pkg/seaice:
4013       add pseudo time stepping for LSOR
4014    o pkg/exch2:
4015       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
4016    o pkg/seaice:
4017       Adding separate sea ice albedo, drag coefficients, and HO in Southern
4018       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
4019    o SingleCpuIO:
4020       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
4021    o pkg/seaice:
4022       put exchanged variable in (local) common block for MPI+Multi-Threads
4023       to work (necessary with exch1, and for now with exch2 too).
4024    o verification: to get more experiments tested with mpi, mth and mpi+mth,
4025      change tiling of:
4026       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
4027       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
4028      update output of exp:
4029       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
4030       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
4031      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
4032                       (note: output.txt generated on faulks using only 1 tile)
4033    o eesupp & mdsio (SingleCpuIO):
4034     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
4035       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
4036       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
4037     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
4038     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
4039       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
4040    o pkg/exch2:
4041     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
4042       read parameter file "data.exch2" if it exists; otherwise try default regular
4043       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
4044     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
4045       with new code (not to be used, just as a backup solution).
4046     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
4047       in utils/exch2/input.
4048    
4049    checkpoint61n (2009/05/12)
4050    o eesupp & mdsio (SingleCpuIO):
4051      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
4052        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
4053        receive real*4 array (instead of real*8) to read/write 32.bit files.
4054        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
4055         and remove new mapping S/R)
4056    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
4057      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
4058        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
4059        when using exch2. Add S/R to map global io-buffer to global model array.
4060      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
4061    
4062    checkpoint61m (2009/04/29)
4063    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
4064      and add 3 other S/R for other types (R4,R8,RS).
4065      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
4066    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
4067     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
4068     - reduce number of macro definitions (keep only those which are used);
4069       can always call directly the corrresponding S/R if needed.
4070     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
4071       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
4072     Fixed wrong type of arg in:
4073       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
4074       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
4075     To fix: global_sum of var in common block is wrong (multi-threaded) in:
4076       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
4077     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
4078    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
4079      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
4080    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
4081    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
4082      edges are closed (zero depth); might happen with "blank tiles";
4083      for now, disabled if using OBCS.
4084    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
4085      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
4086    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
4087      to reduce length of 1.D array print in STDOUT.
4088    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
4089      + use 48 tiles (16x8): this will allow to test "blank tiles".
4090    o start to test MPI + multi-threaded (change testreport to skip tests
4091      where number of tiles do not match).
4092    o genmake2: add option "-omp" to turn on Open-MP ;
4093      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
4094    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
4095      and keep the original tile numbering. Note: compatible with old
4096      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
4097    
4098    checkpoint61l (2009/04/07)
4099    o Overlaps had been forgotten in calculating ijk keys : fixed
4100    o fix cyrus makedepend for gcc 4.4
4101    o experiment fizhi-cs-aqualev20:
4102      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
4103      and generate new output. Note: new output is much closer to the old
4104      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
4105      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
4106    o pkg/fizhi:
4107     - change to avoid indices going deliberately over array-bounds
4108     - remove unnecessary MPI stuff
4109     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
4110     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
4111       does not go over array-bounds and therefore returns reliable output.
4112     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
4113       this S/R has 4 output arguments, which are used inside "get_alarm";
4114       when it is called with the same variable "ndum" in place of several
4115       output arguments, this produces weird side effect inside "get_alarm"
4116      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
4117       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
4118       address) and produces error.
4119    o tools/gemake2: (March 27-29 2009)
4120      with option "-mpi": link *_mpi files from "MODS" dir (this is what
4121      testreport does).
4122    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
4123    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
4124       update lab_sea.lsr & lab_sea.salt_plume results
4125    o pkg/seaice:
4126      Major overhaul of the LSOR solver: change discretization from original
4127      finite differences to finite volume. The old routine is still in the
4128      file seaice_lsr.F and can be turned on with the CPP-flag
4129      SEAICE_OLD_AND_BAD_DISCRETIZATION
4130      Along with this change, the discretization of the strain rates is changed.
4131      The same flag turns on the old discretization in seaice_calc_strainrates.F
4132      All verification experiments with seaice are affected (except for
4133      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
4134      results by setting the above flag.
4135      Further changes involve changes in defaults:
4136      - ALLOW_FLOODING is defined and turned on by default
4137      - SEAICEadvSnow = .true. is now the default
4138      - SEAICEadvSalt = .true. is now the default
4139      - SEAICEadvAge  = .true. is now the default
4140      - SEAICE_clipVelocities  = .false. is now the default
4141                                         (as per J. Zhang's recommendation)
4142      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
4143        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
4144      - seaice_growth: replace computation of UG by a simple copy from wspeed
4145    
4146    checkpoint61k (2009/03/18)
4147    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
4148      seaice_lsr: fixed a few metric terms,
4149                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
4150                  add more debugging diagnostics
4151      seaice_evp: removed superfluous many metric terms of FV discretization
4152                  of stress divergence
4153                  affects lab_sea, lab_sea.hb87
4154      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
4155                  of stress divergence for non-evp solver
4156                  (this part is not tested anywhere)
4157      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
4158                  they were effectively only half slip
4159                  affects lab_sea.hb87
4160      updated all relevant verification experiments (except lab_sea//output_adm.txt
4161        which was left over, but fails at level 7 & 6)
4162    
4163    checkpoint61j (2009/03/17)
4164    o pkg/seaice: turn a few hard wired parameters into run time parameters
4165    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
4166      time in seconds as promised by the usints in seaice_monitor and exf_monitor
4167    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
4168      that are not cubed-sphere grids
4169    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
4170    o pkg/ctrl:
4171      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
4172    o non-hydrostatic (calc_gw.F):
4173      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
4174      update output of exp. global_ocean.cs32x15.viscA4
4175    o remove backward compatibility for thetaMin,phiMin
4176      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
4177    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
4178      interpolated wind field not only for curvilineargrid=.true., but also
4179      for a rotated grid (rotateGrid=.true.)
4180    o pkg/exf: add capability to bypass interpolation for runoff
4181      by setting yet another CPP-flag
4182    o eesupp/src, B-grid exchange:
4183      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
4184    o autodiff
4185      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
4186      allows to switch to single-prec common blocks;
4187      corresponding switch occurs in tamc.h, integer isbyte
4188      TAF store directivs "byte" and "kind" seem equivalent;
4189      Most tamc.h have been updated correspondingly.
4190    
4191    checkpoint61i (2009/02/13)
4192    o autodiff:
4193      fix autodiff_sore/_restore indices for obcs
4194      (spotted by I. Hoteit, M. Mazloff)
4195    o pkg/autodiff, pkg/ctrl:
4196      Add flag to reduce all tapelev I/O to single-prec.
4197      In data.ctrl set
4198        doSinglePrecTapelev = .TRUE.
4199    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
4200      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
4201    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
4202      real fresh water flux (not yet)
4203    o pkg/mdsio & rw:
4204     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
4205     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
4206    o pkg/flt:
4207     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
4208       init_fixed & ini_varia.
4209     - clean-up & simplify linear interpolation S/R:
4210       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
4211     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
4212     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
4213     - add vert. coordinate & horiz. indices to output files.
4214     - change vertical position in initial condition, from index to depth [m].
4215     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
4216       (easier to get to a curvilinear grid) ; delX,delY no longer used.
4217    o pkg/ggl90: a few modifications:
4218     - fix bottom boundary condition, and interpolation of KappaE
4219       near top and bottom
4220     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
4221     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
4222     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
4223    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
4224      (maintain temporary backward compatibility, until next checkpoint)
4225    
4226    checkpoint61h (2009/01/27)
4227    o pkg/diagnostics with "periodic averaging diagnostics":
4228      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
4229    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
4230    o pkg/obcs: fix loop ranges for balancing code
4231    o pkg/flt:
4232     - improve criteria for finding which tile owns a float.
4233     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
4234    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
4235      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
4236      with ocean biogeo)
4237    o pkg/flt:
4238     - do some cleaning and fix the restart ;
4239     - add output.txt in flt_example/results to get this pkg tested.
4240    o genmake2: add an EXTENDED_SRC option and flag.
4241       for now, cannot be turned on on command line (only through genmake_local)
4242    o pkg/mdsio: read/write vector:
4243     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
4244     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
4245       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
4246     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
4247      (drop to 4 digits matching for grad). But this test does not look very
4248      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
4249    
4250    checkpoint61g (2008/12/29)
4251    o pkg/flt:
4252      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
4253       + make OPTIONS file more standard.
4254      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
4255      - fix _BYTESWAPIO CPP-Flag
4256      - standard reading of file-parameter "data.flt"
4257      - fix argument list of S/R FLT_RESTART
4258      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
4259    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
4260    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
4261      a still unfixed compiler/optimization bug
4262    
4263    checkpoint61f (2008/11/21)
4264    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
4265      update results of global_ocean.cs32x15.icedyn test.
4266    o move getcon.F from model/src to pkg/fizhi.
4267    o pkg/exf: add parameter for extrapolation of temp up to the surface
4268       and option to prevent negative evap (in bulk_largeyeager04 only).
4269    o Prather Advection scheme: fix tracer conservation for divergent flow
4270      (e.g., when using NonLin Free-Surface).
4271    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
4272    o gmredi (Visbeck-variable-K):
4273     - add more parameters to Visbeck-variable-K.
4274     - use a 5 points average for dSigmaR in Visbeck-K calculation
4275       (more "homogenous": same stencil and same weights as in dSigmaH)
4276     - update output of ideal_2D_oce experiment.
4277    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
4278      (#undef REAL4_IS_SLOW)
4279     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
4280       coordinate variable
4281     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
4282       (surface forcing fields), removes some of the functionality
4283     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
4284     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
4285       probably not all: copy _RS surface flux fields to RL field before
4286       calling DIAGNOSTICS_FILL
4287     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
4288       real*4 (CALL EXCH_*_RS) versions.
4289     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
4290       (generate new output).
4291    
4292    checkpoint61e (2008/10/23)
4293    o gmredi (Visbeck-variable-K):
4294      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
4295      - change computation of Visbeck-K where Slope > Smax :        
4296        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
4297        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
4298    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
4299      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
4300    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
4301    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
4302      does not become too large (to avoid precision problems in implicit-diffusion
4303      solver); update ideal_2D_oce output.
4304    o pkg ggl90:
4305      - in ggl90_cal.F: compute only one set of visc/diff, used to
4306        step forward TKE/T/S/momentum
4307      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
4308        have Prandlt =1)
4309    o gmredi (fm07):
4310      - add lower limit on Transition layer thickness + lower limit on 1/lambda
4311      - allow to set few more params from data.gmredi
4312    o pkg ggl90:
4313          - add missing sqrt(2) factor in computation of mixing length
4314            scale in ggl90_calc.F
4315            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
4316    
4317    checkpoint61d (2008/09/25)
4318    o adjoint modifs
4319      - adapt to new field rhoInSitu
4320      - allow to revert from StoreDynVars2D, StoreDynVars3D
4321        to individual fields
4322        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
4323    o store 3-D (in-situ) density in commom block (DYNVARS.h)
4324     - save 1 rho computation.
4325     - no longer modify T & S inland when using down_slope pkg.
4326    o gad_som : allow to switch to SOM advection for T & S without corresponding
4327      pickup files (using new S/R: MDS_CHECK4FILE).
4328    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
4329      (for useSingleCpuIO to work in multi-threaded)
4330    o pkg/shelfice:
4331     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
4332       with SHELFICEtopoFile in data.shelfice
4333     - move code for reading ice shelf topography and modifying hFacC into separate
4334       subroutines of the shelfice package
4335     - separate initialisation of "fixed" and "variable" variables
4336     - kTopC is not (yet) replaced by kSurfC, although this is possible
4337    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
4338    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
4339      and rename:
4340      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
4341      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
4342    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
4343    
4344    checkpoint61c (2008/08/30)
4345    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
4346      to add mass source/sink of fluid in the interior (3-D generalisation
4347      of oceanic real-fresh water flux).
4348    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
4349    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
4350    o new pkg: down_slope
4351      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
4352      - presently, modify T & S inland (dwnslp_calc_rho.F).
4353        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
4354      - implementation for ocean in P-coords not tested.
4355      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
4356    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
4357      (to facilitate conversion of oceanic pkg to p-coordinate).
4358    o change FIND_RHO to FIND_RHO_2D :
4359      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
4360    o new pkg: cheapaml
4361    
4362    checkpoint61b (2008/08/05)
4363    o exch2:
4364      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
4365      - no longer depend on the order sequence (N,S,E,W).
4366      - 3rd exchange no longer needed (tested with 24 tiles).
4367      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
4368      - exch_UV_A-grid readily available (but not yet tested).
4369      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
4370      (both are no longer needed) in exch_uv: no effect in forward run; but
4371       get truncation error differences with adjoint exch.
4372    o exch2:
4373     - change index-bounds storage (moved from target to local tile,
4374       more intuitive this way) ; rename/remove some variables.
4375     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
4376    
4377    checkpoint61a (2008/07/29)
4378    o exch2/matlab-topology-generator:
4379      fix bug in index bounds for N-S internal exchange (hard to tell if this
4380      had any effect on the solution).
4381    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
4382      is exceeded
4383    o testreport: modify syntax of awk, so that it works also with
4384      awk, and not only with nawk and gawk
4385    
4386    checkpoint61 (2008/06/24)
4387    o autodiff
4388      Change default for TAF usage by removing argument '-nonew_arg'
4389      This changes TAF subroutine argument list (ordering of active var.)
4390      Omission of this flag leads to incompatibility w.r.t. TAMC
4391      To restore TAMC-compatibility, need following modifs:
4392      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
4393      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
4394      Tested TAF version is 1.9.22
4395      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
4396    
4397    checkpoint60 (2008/06/19)
4398    --->>> This is the last checkpoint for which generating the adjoint
4399    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
4400    --->>> by default.
4401    --->>> Future checkpoints will ommit this flag by default.
4402    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
4403    o pkg/grdchk: Add gradient check to etan0 perturbations.
4404    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
4405    o pkg/autodiff: more flexibility in zeroadj.
4406      model/src: modifying do_oceanic_phys.F accordingly.
4407    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
4408    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
4409      special setup of gmredi for which the adjoint is stable
4410      enough for parameter optimization.
4411    o bridging the gap between eddy stress and GM.
4412      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
4413          along with a change in CPP option (now ALLOW_EDDYPSI).
4414      -> when using GM w/ GM_AdvForm:
4415          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
4416          is applied either in the tracer Eq. or in momentum Eq.
4417          depending on data.gmredi (intro. GM_InMomAsStress).
4418      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
4419      The key modifications are in model/src/taueddy_external_forcing.F
4420      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
4421    
4422    checkpoint59r (2008/05/29)
4423    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
4424      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
4425      fix option to read coriolis(@ cell-corner) from files with CS-grid.
4426    o pkg/mnc: add some attributes to standard 1D-coordinate variables
4427    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
4428      mass points, when using mnc for output
4429      - add runtime parameter (missing_value, missing_value_int) to override
4430        default (which is the value of getcon('UNDEF'))
4431    o pkg/mnc: prepare mnc for the actual use of missing values with the
4432      diagnostics package: small fix in mnc_cw_readwrite.template and more
4433      initialisation of never used fields
4434      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
4435      versions
4436    o pkg/thsice/thsice_ini_vars.F added default initial values so that
4437      thermodynamics sea ice solver does not blow up when some initial fields
4438      are missing.
4439    o move from external_forcing_surf.F to ini_forcing.F
4440      the p-coord. hack consisting in using pLoad to set phi0surf ;
4441      update output of tutorial_global_oce_in_p (affected @ truncation level).
4442    o Freshen up a bit hs94.1x64x5, notably:
4443      remove rotationPeriod and tRef=5*0. (adjoint only), and add
4444      exactConserv=.TRUE.
4445    o pkg/generic_advdiff:
4446      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
4447      applies to files where Temperature & Salinity 2nd Order moments are used.
4448    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
4449      this uses a dynamically allocated internal state data structure
4450      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
4451      and requires a fortran 90 compiler
4452    
4453    checkpoint59q (2008/05/06)
4454    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
4455       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
4456    o Refresh tutorial_global_oce_biogeo, notably:
4457      - change bathymetry (put back seamounts in ACC, use hFacs)
4458      - change EOS (POLY3 --> JMD95Z)
4459      - use Bryan-Lewis vertical diffusivity
4460      - use multidimensional advection
4461      - remove old virtual virtual in dic pkg, now done through ptracer pkg
4462      - change a couple of parameters in dic pkg
4463    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
4464    o pkg/obcs: change default to OBCSfixTopo = .true.,
4465      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
4466      - replace "debugMode" with "debugLevel .GE. debLevB"
4467    o implementation of TAF directives for gchem,cfc,dic
4468    o remove "exp5" (replaced by tutorial_deep_convection).
4469    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
4470      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
4471      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
4472      --> changes results in exp4, seaice_obcs
4473    o tutorial_deep_convection :
4474      update the set-up and increase resolution and domain size ; start
4475      from pseudo initial conditions = output at t=120mn in order to see
4476      something happening when running testreport.
4477    o pkg/seaice: add os7mp as an advection scheme
4478                  add check for advection schemes
4479                  add a flag for restoring T and S underneath sea ice
4480    o pkg/my82: add netcdf-support and diagnostics
4481    o thsice pkg:
4482      - Now hsMax limits snow height by turning it into ice following
4483        flooding scheme (and now conserving energy)
4484      - Slight rewriting of the formula in thsice_calc_thick.F
4485      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
4486      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
4487    
4488    checkpoint59p (2008/04/10)
4489    o gchem / dic / cfc :
4490      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
4491      - add new parameter files: "data.dic" & "data.cfc" ;
4492      - various re-arrangement in initialisation & header file ;
4493      - fix tutorial_global_oce_biogeo for multi-threaded test.
4494    o pkg/dic: test for "pickup_dic" file when restarting ;
4495      if no pickup-file, can restart with a re-initialised pH (same as it did
4496      before) providing pickupStrictlyMatch is set to False.
4497    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
4498      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
4499    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
4500      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
4501    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
4502     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
4503       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
4504    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
4505       scheme to use for vorticty-term ;
4506     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
4507       (with default selectVortScheme, return to original discretisation)
4508     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
4509    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
4510    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
4511      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
4512      also fix diagnostics VISCAHW & VISCA4W.
4513    
4514    checkpoint59o (2008/03/07)
4515    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
4516    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
4517      move a few statemens out the main loop into separate loops
4518    o pkg/shelfice:
4519      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
4520        (kg/m^2/s), does not break tests, because in verification/isomip,
4521        rhoConstFresh=rhoConst (by accident)
4522      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
4523      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
4524        new file model/src/seawater.F, so that they are available for all pkgs.
4525      - convert potential temperature into in-situ temperature. This changes the
4526        isomip tests => update tests
4527    o add a flag writePickupAtEnd (default=true) to be able to suppress
4528      writing a pickup at the last timestep
4529    o tools/mpack-1.6 :
4530      - disable automake (not working) and autoconf (not needed).
4531      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
4532        also cleaner with much less compilation warnings.
4533    o pkg/profiles:
4534      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
4535      (for "less than 32 characters name" compiler requirement)
4536    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
4537      conditions that have a different sampling frequency than S/T/U/V obcs
4538    o pkg/diagnostics (stats-diags):
4539      - fix global Min/Max in case 1 processor get only empty tiles
4540    o genmake2: replace (4 times)
4541         make genmake_tc_1.o >> genmake_warnings 2>&1
4542      with
4543         COMM="$CC $CFLAGS -c genmake_tc_1.c"
4544         echo $COMM >> genmake_warnings
4545         $COMM >> genmake_warnings 2>&1
4546      to make genmake2 always see the value of CC as specified in the optfile.
4547    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
4548      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
4549      - modify verification advect_cs test to test SOM-advection on CS-grid.
4550    o pkg/ctrl:
4551      - Rewrite of ctrl_map_ini_ecco.F,
4552        introducing a generic routine (ctrl_map_ini_gen.F).
4553      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
4554    
4555    checkpoint59n (2008/02/09)
4556    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
4557      number in dedicate array "hdiag":
4558      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
4559        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
4560      - many small changes (integer format) for large number of diagnostics
4561      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
4562        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
4563    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
4564      usingSphericalGrid, this allows to define the rotated grid coordinates
4565      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
4566      geographical coordinates according to the inverse of the rotation defined
4567      by the Euler angles, so that Coriolis parameter and online-interpolation by
4568      exf works with the geographical coordinates on XC/YC/XG/YG.
4569      Naturally, this feature does not work with all packages, so some
4570      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
4571      profiles), because there the coordinates are assumed to be regular
4572      spherical grid coordinates.
4573    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
4574      - introduce isopycnal diffusion coefficient control.
4575    o tools/adjoint_options:
4576      - additional control vector components.
4577    o pkg/mnc: have mnc create marginally meaning full coordinate variables
4578      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
4579    o pkg/mypackage:
4580      - add example of read/write pickup for state-var ;
4581      - add entry points to the main code for state-vars diags & write-pickup.
4582    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
4583      transitions for useExfYearlyFields
4584      - add new subroutine that determines the file to read from for
4585        use*YearlyFields = .TRUE. and .FALSE.
4586      - add a verification experiment to global_with_exf that tests
4587        useExfYearlyFields with USE_EXF_INTERPOLATION defined
4588    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
4589      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
4590      subroutines (which could be generated from a template, because they are
4591      almost identical), for now they are included in obcs_prescribe_read.F for
4592      simplicity
4593    o pkg/exf:
4594      - add a little more diagnostic to exf_interp_read (in analogy to
4595        mds_read_field, can be turned off with debugLevel < debugLevA=1)
4596      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
4597        ugly but fast by unrolling short inner loops, inserting a unroll=8
4598        directive in routine lagran, and splitting a loop and making do while the
4599        outermost loop (the latter requires the intoduction of index arrays)
4600    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
4601    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
4602      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
4603    o verification/seaice_obcs: updated for restart test and latest options
4604    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
4605      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
4606      for now this is only available for the C-grid code and also within
4607      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
4608    
4609    checkpoint59m (2008/01/14)
4610    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
4611      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
4612    o gad_som : fix flux output (& diagnostics) to have same units as other  
4613      advection scheme fluxes (was previously multiplied by deltaT).  
4614    o added verification/seaice_obcs both to test seaice open boundaries
4615      and to provide an example matlab scrpt for generating them
4616    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
4617    o pkg/salt_plume: clean up salt_plume_frac.F to
4618      remove redundancy in PlumeMethod 1 and 4
4619    o pkg/kpp: added saltplume diagnostics
4620    o pkg/obcs and pkg/seaice:
4621      - do not set uice and vice to zero when OB*icefile are unspecified
4622      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
4623      - moved seaice tracer obcs after call to seaice_growth
4624    o pkg/salt_plume: added various options for salt plume depth
4625      criterion and for vertical distribution of the salt
4626    
4627    checkpoint59l (2007/12/18)
4628    o pkg/ptracers: new version of ptracers pickup:
4629      read meta file and write only fields which are needed to restart.
4630      ( same logic as main pickup file ; also using pickupStrictlyMatch )
4631    o pkg/seaice:
4632      - add timescale for melting due to warm mixed layer as a means of
4633        setting SEAICE_availHeatFrac more conveniently
4634      - add a CPP-flag/runtime parameter check for flooding algorithm
4635      - reformulated availHeat in seaice_growth.F to be independent of AREA
4636    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
4637      unit changes
4638    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
4639    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
4640      SX vector computer.
4641    o pkg/seaice:
4642      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
4643        seaice forcing fields can now be read only through pkg/exf
4644      - removed some unused halos
4645    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
4646    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
4647      or U/VICE from U/VWIND before computing U/VSTRESS
4648    
4649    checkpoint59k (2007/11/30)
4650    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
4651      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
4652    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
4653      all experiments pass when compile with un-initialised var. checking option.
4654    o added pkg/salt_plume
4655    o script to test restart (for now, in MITgcm_contrib/jmc_script)
4656    o pkg/seaice: new read/write pickup version.
4657      read meta file and write only fields which are needed to restart.
4658      ( same logic as main pickup file ; also using pickupStrictlyMatch )
4659    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
4660    o lab_sea.hb87: modify the domain & update output.hb87.txt :
4661      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
4662      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
4663      process. Fixed here by closing the domain at the Northern boundary.
4664    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
4665    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
4666      a set of consecutive levels in/from a 3-D array.
4667    o pkg/ptracers:
4668      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
4669      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
4670    
4671    checkpoint59j (2007/11/09)
4672    o in pkgs: dic, obcs, offline, rbcs:
4673      standard way to compute coeff. for time interpolation between 2 time reccords
4674      which retains full precision (& make results less dependent on compiler).
4675      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
4676    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
4677      packages instead of reading ice cover and wind speed separately
4678    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
4679     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
4680      to allow to compile customized code before the update)
4681    o cleaning-up:
4682      - fix CPP instruction syntax in pkg/obcs
4683      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
4684        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
4685      - fix some threads issue in IO parts.
4686    o pkg/dic:
4687      - add tons of "_d 0" (--> much better testreports !)
4688       and then update outputs of tutorial_global_oce_biogeo
4689    o pkg/mom_fluxform:
4690      add a special version of momentum advection intended to conserve momentum
4691      next to a bathymetry step or a coastline edge. (default = off = #undef)
4692    o new read/write pickup version:
4693      - for now, only implemented for main (mdsio) pickup file.
4694      - write out only what is needed to restart; merge pickup_nh , pickup_ph
4695        and main pickup together.
4696      - read meta file; read only what is needed to restart; stop if a field
4697        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
4698        if it make sense (even if the restart is not perfect).
4699      - if no meta file, assume that pickup to read corresponds exactly to
4700        a pickup that would currently be written.
4701      - read pickup written in the old format (until checkpoint59i) if it
4702        recognizes an old meta file (no field-list).
4703      - add a meta file in exp. which starts from a pickup: 2 cases:
4704        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
4705         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
4706        b) a meta file describing the content of the associated pickup file
4707         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
4708    o pkg/mdsio & pkg/rw:
4709      - new routine to read a meta file ; new set of routine to read
4710        Multiple-fields file (with meta file).
4711    o added open boundary conditions capability for seaice
4712        HSNOW, HSALT, UICE, and VICE
4713    
4714    checkpoint59i (2007/10/21)
4715    o adjoint:
4716      * fix multiDimAdvection adjoint
4717        (partial recomputation problem by TAF for fVerT(:,:,kDown)
4718        and comlev1 size definition (maxpass vs. max. number of tracers)
4719      * verification/global_ocean.90x45x15 adjoint now tests
4720        NLFS and multiDimAdvection using DST3 (=30)
4721      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
4722    o pkg/kpp: add "_d 0" to real constant (if missing);
4723      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
4724      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
4725    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
4726      for internal parameters related to restart process (formerly from PARAMS.h)
4727      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
4728    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
4729      as argument. (only atm2d & obcs write_pickup have not yet been updated)
4730    o pkg/monitor:
4731      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
4732      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
4733      - account for deep Atmosphere factor and density factor (anelastic)
4734    o added open boundary conditions capability for seaice HEFF and AREA
4735    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
4736      thermodynamics
4737      - requires a little reorganization, which affects the testreport results
4738        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
4739        so that now the conservative form is tested
4740      - add a few comments
4741    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
4742    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
4743    o add new diagnostics to seaice: advective, diffusive fluxes (only for
4744      multidim-advection, for scheme 2 they are not filled) and transports,
4745      thermodynamic growth rates
4746    o change units of EmPmR (inside the code, + within coupling interface)
4747      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
4748      Affects results @ truncation level (cg2d match) and update output of
4749       experiments: lab_sea(6), global_ocean.90x40x15(10),
4750      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
4751      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
4752      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
4753      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
4754    
4755    checkpoint59h (2007/09/29)
4756    o pkg/exf:
4757      - improve vectorization by moving if-statement out of loops in
4758        exf_mapfields, exf_radiation
4759      - exf_bulkformulae.F: introduce 2D fields and vectorize code
4760    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
4761    o testreport:
4762      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
4763        monitor & update offline_exf_seaice exp. output.
4764      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
4765    o pkg/seaice:
4766      - bug fix in the evp solver: boundary conditions were affected be
4767        masking of zMax/zMin (changes results)
4768      - minor bug fix in boundary conditions in seaice_calc_strainrates
4769        (changes results for no_slip)
4770      - seaice_lsr.F: make interpolation of eta dependent on boundaries
4771      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
4772      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
4773        stress formulation and no-slip boundary conditions
4774    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
4775      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
4776    o pkg/seaice: a first HSALT time stepping equation has been checked in
4777    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
4778      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
4779      without requiring DO-IF statements
4780    o pkg/thsice:
4781      use continuous power-law function for partition of energy between lateral
4782      melting/freezing and thinning/thickening ; old code using step function
4783      still available with #undef THSICE_FRACEN_POWERLAW
4784      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
4785    o testreport: change AD testing : check against results/output_adm.txt
4786      using same scripts as for forward test.
4787    
4788    checkpoint59g (2007/09/17)
4789    o adjoint testing: in preparation for changing testreport:
4790      - output format: cost and grad written on separated lines
4791      - ad output results in directory "results" (instead of "results_ad")
4792    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
4793    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
4794    o pkg/ecco: allow user defined cost function contributions
4795    o testreport:
4796      Allow to choose (per experiment) the list of tested output variables
4797       and the main variable (used to issue a pass/FAIL ) ;
4798      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
4799      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
4800      Also modify printing of summary:
4801       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
4802       b) echo the list of tested variables in the individual summary.txt of
4803          each experiment.
4804    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
4805      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
4806      (but still depend on the tile decompostion of the domain).
4807    o pkg/seaice: change a discretization detail to make the B-grid code
4808      "more symmetric". This change is likely to remove all "ridges/leads" that
4809      where quasi-aligned with the grid in B-grid solutions. It may also be
4810      the solution to the stress coupling issues with the B-grid.
4811    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
4812      remove .cvsignore from input dir. (since testreport no longer run here).
4813    o pkg/thsice:
4814     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
4815     - fix reshaping of sea-ice just after advection:
4816       melt all the ice only if ice-volume is too small.
4817     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
4818       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
4819     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
4820    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
4821      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
4822    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
4823      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
4824      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
4825      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
4826      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
4827      -> update output.txt
4828    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
4829     this affects truncation error: -> update output.txt of exp:
4830      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
4831      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
4832    
4833    checkpoint59f (2007/08/21)
4834    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
4835    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
4836      a bounded range (in forward mode)
4837    o pkg/ecco, ctrl, autodiff and mom_common:
4838     internal parameter controls, completements of implementations
4839    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
4840    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
4841      (not seem any difference in testing results).
4842    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
4843       at face corners.
4844    o pkg/generic_advdiff:
4845     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
4846      loop range indices for computing vertical advection tendency
4847      and do the calculation in the interior only (no overlap) ;
4848      for now, only implemented for SOM advection (to save CPU time).
4849     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
4850    o exch2 adjoint
4851      First set of changes:
4852      - add exch2 hand-written adjoint templates
4853      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
4854        This will require cleanup in pkg/autodiff/*.F
4855        (changed routines currently kept separate in verif. code/)
4856      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
4857        that used to hide exch2 or cubed-sphere specific code
4858        (commented via 'cph-exch2')
4859    o pkg/seaice
4860      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
4861    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
4862       output of global_ocean.cs32x15.thsice .
4863    
4864    checkpoint59e (2007/07/26)
4865    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
4866      for B-grid vector (not yet tested) and C-grid vector (<- only used
4867      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
4868    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
4869      (#ifdef ALLOW_SALT_PLUME)
4870    o gather_2d/scatter_2d: removed halo regions
4871    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
4872      scheme and the corresponding test case (under front_relax dir). For now,
4873      only available with Skew-flux form and not yet tested in realistic set-up.
4874      adjoint: store directives updated, but gradient checks deteriorated,
4875      so maybe GM/Redi adjoint is now broken.
4876    o seaice adjoint
4877      * add AREA, HEFF, HSNOW as control variable
4878        (should not change lab_sea results)
4879      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
4880    o pkg/seaice:
4881      * added computation of saltFlux in seaice_growth;
4882        For time being, sea ice salinity is assumed constant
4883        contribution of snow flooding to freshening of sea ice is neglected.
4884        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
4885        defaults to 0.0 in order to maintain backward compatibility.
4886        Typical values for SEAICE_salinity are 4 to 10 g/kg.
4887      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
4888      * added SEAICE_availHeatFrac, which specifies fraction of surface level
4889        heat content used to melt or grow ice
4890      * commented out cap of HICE: it helps keep ice thinner
4891      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
4892      * applied OBCS T/S mask to HEFFM sea ice mask
4893    
4894    checkpoint59d (2007/06/21)
4895    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
4896     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
4897     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
4898    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
4899     and change default value of parameter "GM_Small_Number";
4900     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
4901       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
4902       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
4903    o pkg/ecco: cost function when applying pkg/smooth to controls
4904    o pkg/ctrl: add forcingPrecond run time parameter
4905    o pkg/seaice:
4906     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
4907     - fix bug in metric terms of u-equation in LSR solver (implicit part),
4908       changes verification/lab_sea
4909     - rearrange implicit part of u-equation in LSR solver to make it easier to
4910       read, understand, and debug. This causes changes at the truncation level.
4911     - fix (serious) bug in the boundary conditions (sign error in the implicit
4912       part) of the LSR solver. Changes all LSR results.
4913     - fixed problem with HSNOW initialization to avoid thick snow when AREA
4914       is initilized with small values - does not change lab_sea results.
4915     - added HsnowFile initialization capability
4916    o pkg/smooth: addition to model/src and pkg/ctrl so allow
4917     initialization of pkg/smooth and application to control vector
4918    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
4919    o dependencies: pkg/profiles requires pkg/cal
4920    o pkg/profiles:
4921     - added option ALLOW_PROFILES_GENERICGRID
4922         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
4923         that interpolation information (grid points and coefficients) is provided
4924         within the netcdf input files.
4925         -> sample matlab scripts can be found in MITgcm_contrib/gael
4926         that allow you to prepare netcdf input files.
4927     - also modified: cleaner include statements, cleaner error print statements,
4928       cleaner stops when error, and more tests of the netcdf input files consistency.
4929    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
4930    o pkg/seaice:
4931     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
4932       requires a new routine: seaice_diagnostics_fill.F
4933     - make sure that seaice does not move if not forced (pressure replacement
4934       method, Hibler and Ip, 1995), changes results
4935     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
4936     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
4937       It is turned off by default (=-1.), because it changes the results.
4938     - make it possible to read AREA from a file, too.
4939    
4940    checkpoint59c (2007/06/04)
4941    o add S/R and diagnostics for oceanic mixed-layer depth
4942    o move GMRedi call after all vertical mixing schemes (including KPP)
4943    o pkg/thsice:
4944     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
4945      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
4946    o pkg/obcs:
4947     - bug fix for balance code
4948    o pkg/seaice:
4949      - allow values of SEAICE_elasticParm > 1
4950      - add new parameter SEAICE_evpTauRelax as an alternative
4951        to SEAICE_elasticParm
4952      - make lsr boundary conditions free slip (by default), changes result
4953      - add code for no slip boundary conditions for lsr
4954      - set minimum of zeta to zero (and not 4e8) (changes results)
4955      - add a cap on AREA after advecting AREA if seaice_growth is not called
4956    o change calculation of Visbeck K:
4957      - no longer depend on tapering scheme; instead, compute slope (limited
4958        by GM_maxSlope). this is equivalent to what was comuted before with
4959        clipping or linear tappering.
4960      - fix vertical averaging (wrong by 1/2 level)
4961      - leave the old version (but will not be maintained) within
4962        #ifdef OLD_VISBECK_CALC / #endif
4963      - update output of exp. ideal_2D_oce
4964    o change error catch in calc_r_star to improve vectorization
4965    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
4966      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
4967    o adjoint:
4968      Re-organized adjoint checkpointing according to Matt Mazloff
4969      (but with modifs/completions/cleanups)
4970      Storing is now bundled into large arrays to optimized I/O
4971      (and second step in cleanup of the_main_loop)
4972    
4973    checkpoint59b (2007/05/16)
4974    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
4975      - export/import (between ocean & coupler) fields needed for ocean DIC.
4976    o pkg/seaice:
4977      - get rid of three more exchanges seaice_calc_viscosities (required
4978        different loop boundaries in seaice_lsr and seaice_ocean_stress)
4979      - bug fix in seaice_ocean_stress (update of lab_sea required)
4980      - reduce loop boundaries to necessary minimum also in seaice_evp
4981      - go back to the old way of computing deltaC/Z as the adjoint likes that
4982        better
4983    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
4984      passive tracer to an Age Tracer) + update output.txt
4985    o pkg/exf:
4986      - implement A-grid / C-grid selection for wind-stress input files.
4987      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
4988      for now, in exf_bulk_largeyeager04.F only :
4989      - change implementation for case where windspeed + 2. components wind-stress
4990        are read-in. AND use rhoConstFresh to convert evap.
4991    o pkg/seaice:
4992      - use correct EXCH_UV for wind-forcing (on A-grid).
4993      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
4994        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
4995    o pkg/exf:
4996      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
4997      EXF_INTERPOLATION:
4998      - merge global_with_exf/code version of exf_interp_read.F
4999        to the main code ;
5000      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
5001        reading the file ; Important: This options needs to be defined to recover
5002        previous code.
5003        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
5004      - no longer loose real*8 precision along the way when using exf_iprec=64.
5005    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
5006      - change discretisation of evp-solver in order to avoid another exchange
5007        (changes lab_sea) and clean up a little
5008      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
5009        help the adjoint (this also changes the results slightly)
5010      - add a few "_d 0" where they had been missing in seaice_evp.F
5011      - cleaning up: remove unused seaice_calc_rhs.F
5012    o pkg/exf: some cleaning-up:
5013      - change various "constants" into runtime parameters
5014      - cleaned-up Large&Yeager04 routine which should eventually
5015        replace exf_bulkformulae.F (changed names of S/R and CPP)
5016        and merged various ALLOW_ATM_WIND options
5017     only used with thsice pkg (in thsice_get_exf.F):
5018      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
5019        which are used when useStabilityFct_overIce=TRUE (= the default)
5020      - change default values of ice & snow emissivity and scale downward LW
5021        by ice & snow emissivity.
5022    o pkg/thsice:
5023     fix few little problems, in thsice_calc_thickn.F:
5024      - growth vertically (and not laterally) if iceFrac == iceMaskMax
5025      - melt only laterally if hIce < hThinIce (as the comments say)
5026      and in thsice_extend.F:
5027      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
5028      - start to form ice as soon as the minimum ice-volume is reachable.
5029     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
5030      and cpl_aim+ocn
5031    o pkg/kpp
5032     - move computation of surface related input fields to KPP into a new
5033       subroutine kpp_forcing_surf.F
5034     - remove wrong (within bi,bj loops) EXCH calls.
5035     - little cleaning (add argument myThid in last position, cvs header ...)
5036     - for now, fix conservation problem by exchanging KPPviscAz (may not
5037       be the best fix)
5038    o pkg/seaice
5039     - check for inconsistent evp parameter/cpp-flag combination
5040     - remove leftover errIO flat for obsolete name list error handling
5041    o OpenAD
5042     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
5043    
5044    checkpoint59a (2007/05/01)
5045    o pkg/seaice: some parameter clarifications and a little bit of clean up
5046    o pkg/thsice: rename run-time parameters:
5047       himin       -> hIceMin
5048       himin0      -> hThinIce
5049       hihig       -> hThickIce
5050       i0          -> i0swFrac
5051       transCoef   -> bMeltCoef
5052       frac_energy -> fracMelting
5053      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
5054       with default values (for now) that do not change the results.
5055      remove old version of thsice vars advection in pkg/seaice.
5056    o in FFIELDS.h:
5057      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
5058      - make pLoad & sIceLoad always available (but still only used if
5059         ATMOSPHERIC_LOADING is #define).
5060    o pkg/kpp: replaced _KPP_RL with _RL
5061    o bug fixes for vertical diffusivity computations when both KPP and
5062        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
5063        are no longer updating the vertical diffusivity array
5064        (passed as argument) but are (re-) setting those arrays.
5065    o pkg/seaice: fix bug in evp solver, while doing that
5066      - change (improve?) discretization of stress computations for both
5067        cgrid-lsr and evp solver
5068      - add a new routine to compute strain rates
5069      - the above changes lab_sea results
5070      - add no slip conditions for evp solver (off by default), lsr-version
5071        may follow
5072      - fix exchange for shear at Z-points (does not change lab_sea)
5073      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
5074        (to force the user to pick a time step since there is not "safe" way
5075        of choosing it)
5076      - add principal stress diagnostics
5077      - rearrange fields for evp a little to avoid having to call a: too many
5078        exchanges and b: exchanges for stress trensor components which we do
5079        not have.
5080      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
5081        of evp, complete rewrite for lsr case (latter is does not yet work
5082        in all cases)
5083    o pkg/kpp: add code to have mixing in shelf ice caverns
5084      - add myThid to all kpp routines (long overdue)
5085    
5086    checkpoint59 (2007/04/19)
5087    o pkg/exf:
5088      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
5089        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
5090      - move exf header files from lower_case.h to UPPER_CASE.h ;
5091        add missing cvs Header & Name
5092      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
5093      - add namelist param. selectStressGridPosition, exf_monFreq
5094      - retire many _CLIM routines, and remove data.exf_clim
5095        + params moved to data.exf
5096        + climsst, climsss now handled by exf_set_gen, i.e.
5097          climss?period=0 refers to constant field,
5098          climss?period=-12 to monthly forcing
5099      - split up namelists in data.exf
5100    o pkg/seaice:
5101      - remove seaice_exch and seaice_exch_uv
5102      - remove superfluous exchange of theta
5103      - add myThid to seaice_budget_ocean/ice
5104      - add new interface for atmospheric wind forcing (C-grid only)
5105        + new routine
5106        + two new field (taux, tauy for stress over ice)
5107        + removed one global field (DAIRN) for C-grid case only
5108    o pkg/thsise
5109      - 2nd set of modifs for thsice adjoint in conjunction with exf
5110    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
5111    
5112    checkpoint58y_post (2007/04/15)
5113    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
5114      vertical diffusivity, similar to that in MOM4; turned on using
5115      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
5116      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
5117    o Added capability for 3D specification of background vertical diffusion
5118      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
5119      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
5120      "data" file that contains the 3D vertical diffusivity coefficients.
5121    o ice dynamics (pkg/seaice) with thsice thermodynamics:
5122      - add code within pkg thsice to advect & diffuse sea-ice fields
5123      similar to (and will replace) what has been added in  seaice_advdiff.F,
5124      but: - conserving Mass, Heat & Salt.
5125           - better when using non-linear advection scheme (not yet fully tested)
5126           - can also be used in atmospheric set-up (for now, only the diffusion).
5127    
5128    checkpoint58x_post (2007/04/04)
5129    o IO option for global-file compact format:
5130      - add options when generating topology (utils/exch2/matlab-topology-generator)
5131      - add I/O capability (pkg/mdsio).
5132      - adapt utils/matlab/rdmds.m to read this format.
5133      for now long-line format not yet supported by pkg/mdsio (& exch2).
5134    o shelfice: add a few diagnostics
5135    
5136    checkpoint58w_post (2007/03/13)
5137    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
5138      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
5139      (and replace horiVertRatio in NH code).
5140      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
5141                         and tutorial_plume_on_slope (sensitive to truncation)
5142    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
5143      directly to drive seaice model (C-grid only)
5144    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
5145     - reintroduce computation of wind from stress,
5146     - compute tau (in exf_bulkformulae.F) from windstress averaged to
5147       mass points to avoid tau = 0
5148     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
5149    o rdmnc.m: make it work with "global" files created with gluemnc
5150    o rdmnc.m : some improvements in dealing with singleton dimension
5151      (tested on all testreport mnc output files).
5152    o genmake2: disable pkg/profiles if netcdf test fails.
5153    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
5154    o move call to cal_readparms up to make calendar parameters/variable available
5155      to all packages
5156    
5157    checkpoint58v_post (2007/02/08)
5158    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
5159      useDynP_inEos_Zc tested.
5160    o pkg/exf: changes to properly interpolate/mask/scale initial fields
5161    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
5162      and portions thereof.  See read_cs.txt for description and examples.
5163    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
5164      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
5165      following the great-circle arc between those 2 points.
5166    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
5167      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
5168    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
5169     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
5170     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
5171     - still needs work (not working with some options ; efficiency to improve)
5172       and serious testing.
5173     - use this scheme for temperature & salinity in 2 advection test exp.:
5174       advect_xy & advect_xz, respectively.
5175    
5176    checkpoint58u_post (2007/01/12)
5177    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
5178    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
5179    o testreport: add option "-skipdir" to skip some test.
5180    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
5181      momentum calculation.
5182    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
5183    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
5184      remove checkpoint.F and the_correction_step.F (no longer used);
5185      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
5186    o add option (linFSConserveTr) to correct for tracer source/sink due to
5187      Linear Free surface
5188    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
5189    o pkg/thsice: fix reading mnc-pickups
5190    
5191    checkpoint58t_post (2006/12/30)
5192    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
5193    o pkg/mdsio:
5194     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
5195       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
5196       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
5197     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
5198     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
5199       either MDS_READ_FIELD or MDS_WRITE_FIELD )
5200     - new S/R (to replace MDSWRITEMETA), which allows to write more
5201       informations (variable names, time ...) to meta files.
5202     - modify rdmds.m to give back the meta file content.
5203    o pkg/diagnostics: change vertical interpolation to be safer, and more
5204       flexible (define p-levels to interpolate to in data.diagnostics);
5205      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
5206       diagnostic pointer.
5207    o pkg/seaice: more cleaning up of seaice_growth, added many comments
5208    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
5209    o fix multi-category seaice:
5210     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
5211       SEAICE_MULTICATEGORY
5212     - fix short wave heat flux
5213    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
5214       and allow to use EVP solver. Change forward lab_sea: test both EVP
5215       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
5216    o Initial check-in of lab_sea adjoint
5217      (very similar to natl_box_adjoint/code_seaice)
5218      * used C-grid and EVP solver
5219      * used KPP, GM/Redi
5220      * uses inAdExact=.TRUE.
5221      * gradient checks fail for both ADM and TLM
5222        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
5223        f.d. gradients actually seem more problematic than ADM, TLM gradients;
5224        issue is related to forward mismatch between g77 an ifort
5225    o pkg/seaice: overhaul of thermodynamics
5226     - growth.F and groatb.F are replaced by new routine seaice_growth.F
5227     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
5228     - move a few global fields out of SEAICE.h into seaice_growth.F and
5229       make them 2D (FICE/QNETO/ ...)
5230     - remove FO (it is the same as QNETO)
5231     - introduce a few local fields to avoid modifying external fields such
5232       as atemp, etc.
5233    
5234    checkpoint58s_post (2006/12/11)
5235    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
5236      changed exf_set_gen.F so that
5237        genperiod=0 means input file is one time-constant field and
5238        genperiod=-12 means input file contains 12 monthly means
5239    o CG2D: use pre-computed solver main-diagonal (stored in common block);
5240      this affects truncation error ; generate new output file for exp. which
5241      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
5242        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
5243        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
5244        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
5245        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
5246        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
5247    o start implementation of deep-atmosphere and anelastic formulation
5248    o verification: remove 2nd copy of input files and use script "prepare_run"
5249      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
5250    o mom_common/vecinv/fluxform: fix a few initialisation isssues
5251    o profiles: fix for multithreaded case
5252    
5253    o diagnostics: rename few diags:
5254      s/'PRESSURE'/'RCENTER '/g
5255      s/'TICE    '/'oceFreez'/g
5256      s/'TAUX    '/'oceTAUX '/g
5257      s/'TAUY    '/'oceTAUY '/g
5258      s/'SWFLUX  '/'oceQsw  '/g
5259      s/DIFx/DFxE/g
5260      s/DIFy/DFyE/g
5261      and add few ocean-forcing diagnostics:
5262      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
5263    o modifications to pkg/seaice/growth.F and budget.F, which change results of
5264      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
5265      as actual snow thickness.  It now refers everywhere to effective snow
5266      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
5267    
5268    checkpoint58r_post (2006/11/17)
5269    o modifications to pkg/seaice/growth.F, which change results of
5270      lab_sea experiment: fixes pertain to melting snow over open water, to
5271      masking EVAP under sea ice, and to using the correct AREA variable for
5272      computations of EVAP, PRECIP, HSNOW, and GHEFF
5273    o add ability to read bathy, salt, and theta using MNC (off by def)
5274    o add flooding algorithm and advection of HSNOW for pkg/seaice;
5275      both are turned off by default and do no change any results
5276    o seaice advection with pkg/thsice: a step toward the use of non-linear
5277      advection scheme, but #ifdef or commented out for now (requires more EXCH).
5278    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
5279      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
5280      in natl_box (affects results @ truncation level: update output.txt)
5281    o multi-threading and IO:
5282      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
5283      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
5284        (needed to work with SingleCpuIO): tested in all verif. exp.
5285    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
5286      affects the results (but none of the verification test uses this scheme).
5287    o Adding some pkg/diagnostics capability to pkg/seaice
5288      (will certainly be subject to changes)
5289    o ctrl: adding new control variables:
5290      lwflux, lwdown, evap, snowprecip, apressure, runoff
5291    
5292    checkpoint58q_post (2006/10/20)
5293    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
5294      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
5295      high_res_cube configuration by 4% on Columbia.
5296    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
5297      add (in global_with_exf/code) a version of EXF_INTERP_READ without
5298      dynamical allocation (seems to work in multi-threaded).
5299    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
5300      single CPU io) so that TAF does not have to see EESUPPORT.h
5301    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
5302    
5303    checkpoint58p_post (2006/09/08)
5304    o obcs: stop if obcs is used with useCDscheme = .true.
5305    o shelfice:
5306     - fix a sign error so that no slip at shelfice interface works
5307     - remove stop for combination non-hydrostatic code and shelfice. That does
5308       not mean, that the results are correct, but at least they are numerically
5309       stable
5310    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
5311    o added adjoint exch routined for all exch*3d* routines
5312      and updated flow directives
5313    
5314    checkpoint58o_post (2006/08/28)
5315    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
5316      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
5317    o change controling S/R for writing pickup file (new S/R do_write_pickup)
5318      and clean-up reading/writing of pickup files.
5319    o fix local version of read/write pickup (NH part) in rotating_tank/code
5320    o simplify EXCH interface:
5321     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
5322     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
5323    o added the regrid package
5324    o shelfice:
5325     - add a simple boundary layer scheme to reduce noise
5326     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
5327    
5328    checkpoint58n_post (2006/08/14)
5329    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
5330       local variable (not in common block).
5331    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
5332      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
5333      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
5334        to work with SingleCpuIO.
5335    o add "_d 0" to real constant of pkg/cfc subroutines ;
5336       update exp. cfc_exemple & tutorial_cfc_offline output files.
5337    o multi-threading and IO:
5338      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
5339        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
5340      - barrier before and after reading.
5341      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
5342      - avoid using MDS_WRITELOCAL for LAND pkg output.
5343      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
5344        common-block variables ; Allows multi-threading with master-thread IO.
5345    o change default MAX_NO_THREADS from 32 to 4 ;
5346      and stop cleanly when MAX_NO_THREADS is too small.
5347    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
5348    
5349    checkpoint58m_post (2006/07/17)
5350    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
5351       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
5352    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
5353       keep global_ocean.90x40x15 (for AD testing) with former secondary test
5354       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
5355    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
5356        add MITgcm_tutorials (= code + all the tutorials)
5357    o ecco, option to compute cost for total ssh (mean+anom)
5358    o consistent with addition of ptracer and ssh in pkg/profiles
5359    o profiles: adding ptracer and ssh
5360    o testreport: change multi-test output-file name
5361      (from output.txt.{name} to output.{name}.txt)
5362    o profiles: now ok for mutli-tiles case
5363    o seaice: add 4 parameters for different advection schemes for area,
5364      (effective) seaice thickness, enthalphy, and snow height. Their default
5365      is the standard parameter SEAICEadvScheme
5366    o calc_gw:
5367     - add cosFacU in zonal viscous flux (harmonic.visc.).
5368     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
5369       of tutorial_plume_on_slope.
5370    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
5371    o calc_gw: true flux-form, account for horizontal grid spacing.
5372      update rotating_tank results, but not plume_on_slope (affected at
5373      truncation level, 11 digits).
5374    
5375    checkpoint58l_post (2006/07/12)
5376    o calc_gw:
5377     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
5378     - remove side-drag for now (need to fix it); update plume_on_slope results.
5379     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
5380    o commit code to make SST/SSS weights spatially variable
5381      (based on either variable in-situ or variable initial T/S weights)
5382    o pkg/ecco:
5383      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
5384        now based on horizontally varying weights wthetaLev, wsaltLev
5385      * cost_averagesflags now returns year indices in addition to day, month
5386      * sflux balance is performed on annual basis
5387        (sflxumm, sfluxmm2, bal_sfluxmm)
5388      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
5389        including separate counting and multipliers
5390    o pkg/rbcs
5391      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
5392    
5393    checkpoint58k_post (2006/07/06)
5394    o testreport:
5395     - always build in dir. "build" (if not there, mkdir build instead of building
5396       & running in input)
5397     - run in dir run (if it exists), in build otherwise.
5398     - call prepare_run (if input/prepare_run exists)
5399     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
5400    o pkg/exf modifications to interpolation and rotation routines for more
5401       reasonable treatment of North Pole singularity: for tracers North Pole
5402       value is set to northernmost zonal-mean value, for zonal velocity it is
5403       set to zero, and for meridional velocity it is set to northernmost value.
5404    o pkg/exf/exf_check_range.F
5405     - add tile index to diagnostics and move stop statement to the very
5406       end of the routine.
5407    o pkg/diagnostics: (diagnostics_main_init.F)
5408      define title of isomorphic variables according to the current config.
5409    o pkg/thsice with pkg/seaice dynamics:
5410    - fix domain of computation (interior only, required for exf) and do exchanges
5411    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
5412    o towards a standard way of dealing with multi-threading in MONITOR
5413      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
5414    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
5415       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
5416    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
5417    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
5418    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
5419       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
5420    o tracer advection:
5421     - clean-up and simplify calc_common_factors.F
5422     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
5423       advection subroutine (but still not used within DST advection S/R)
5424    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
5425    
5426    checkpoint58j_post (2006/06/15)
5427    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
5428      from file (collects calls previously in FORWARD_STEP)
5429    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
5430    o adjoint store dir. adjusted accordingly
5431    o genmake2
5432      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
5433    
5434    checkpoint58i_post (2006/06/14)
5435    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
5436      on wind stress (SEAICEstressFactor defaults to 1.)
5437    o Total number of Timers is finite (<=40): comment out 2 non-essential one
5438      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
5439    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
5440      on CS-grid: no longer loosing mass.
5441    o exf & curvilinear-grid: no longer modify longitude xC & xG.
5442    o pkg/ggl90: fix sloppy output and fix a bug
5443    o pkg/seaice: added SEAICEuseEVPpickup parameter
5444      - Set to false in order to start EVP solver with
5445        non-EVP pickup files when using SEAICEuseEVP
5446      - fix sign error in diffusion in seaice_calc_rhs
5447    
5448    checkpoint58h_post (2006/06/07)
5449    * Modifications for bottom topography control
5450      o replace hFacC by _hFacC at various places
5451      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
5452      o add non-self-adjoint cg2d_nsa
5453      o update autodiff support routines
5454      o re-initialise hfac after ctrl_depth_ini
5455      o works for 5x5 box, doesnt work for global_ocean.90x40x15
5456    * Adding verification for 5x5 box (4-layer) bottom topography control
5457    
5458    checkpoint58g_post (2006/06/07)
5459    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
5460       used for mean seasonal cycle, mean diurnal cycle); add an example
5461       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
5462    o pkg/ggl90:
5463      - add parameter (minimum surface kinetic energy)
5464      - fix bug (avoiding division by zero)
5465    o couple pkg/thsice to pkg/seaice:
5466      - modify advection in seaice to accomodate new scalar fields to be advected
5467      - only muliDimAdection scheme work with seaice/thsice
5468      - mapping of thsice-variables to seaice-variables, back and forth
5469      - does not break the verification experiments, but does not give the
5470        desired results either
5471    o pkg/seaice
5472      - make (default) second order advection a bit less confusing?
5473    
5474    checkpoint58f_post (2006/06/05)
5475    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
5476      to pkg/seaice):
5477      - new routines thsice_map_exf and thsice_get_exf provide the interface
5478      - add an additional formal parameter to thsice_solve4temp
5479    o pkg/exf:
5480      - add new fields wspeed, snowprecip (to be able to couple to thsice)
5481      - correct Stefan-Boltzmann constant
5482      - new parameter for longwave surface emittance
5483      - separate some stuff from exf_bulkformulae into new routines  
5484        exf_radiation, exf_wind
5485      - add new parameters and constants: longwave emissivity for ocean, ice
5486        and snow, evaporation parameters over ice
5487      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
5488        either wind from stress or stress from wind
5489    o pkg/thSIce:
5490    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
5491    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
5492       and THSICE_CALC_THICKN
5493    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
5494    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
5495      to make debugging easier.
5496    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
5497    o pkg/bulk_force:
5498      - clean-up comments and parameters ;
5499      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
5500    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
5501      generate new output for test-experiment: aim.5l_cs.thSI
5502    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
5503      testreport accordingly
5504    
5505    checkpoint58e_post (2006/05/17)
5506    o SEAICE_CGRID adjoint done
5507    o R_STAR adjoint implemented.
5508      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
5509      * need to sort out init. of h0facc, etc.
5510    o Make pkg/profile fully independent of ecco,cost, etc. stuff
5511      to be able to use it in pure forward.
5512    
5513    checkpoint58d_post (2006/04/21)
5514    o upgrade simple test-experiment to tutorial example:
5515     step.1: duplicate the experiment and (step.2) will remove the old copy.
5516      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
5517      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
5518      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
5519      tutorial_global_oce_biogeo    <- copy of dic_example
5520      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
5521      tutorial_plume_on_slope       <- copy of plume_on_slope
5522      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
5523      tutorial_global_oce_optim     <- empty for now (David ?)
5524      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
5525     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
5526    o correct a sign problem in cost_scat.F
5527    o obcs and ptracers: fix boundary conditions for advections schemes
5528      with larger stencil
5529    o thsice adjoint: start
5530    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
5531      completeness
5532    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
5533      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
5534    o ptracers adjoint:
5535      * avoid extensive recomputatations
5536      * fix missing re-init. of gptr (missed by TAF)
5537    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
5538      me to turn off the excessive output to STDOUT that this package produces
5539    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
5540      and add those terms in Vector-Invariant formulation.
5541    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
5542      if the control period (xx_hfluxperiod etc) is 0
5543    o in profiles pkg, clean routines and fix details
5544    o in ecco pkg, reading ssh data:
5545      fix problem in case the model does not start at iter0=0
5546    o fix mnc-pickup/restart for ptracers
5547    o new package prifiles:
5548      code to compute profile-based cost by Gael Forget
5549      (modifs in ecco, ctrl, autodiff)
5550    o Benign bug fix in initialization (spotted by M. Mazloff) of
5551      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
5552    
5553    checkpoint58c_post (2006/03/23)
5554    o adjoint: finish NLFS adjoint and provide reference output in
5555      verification/global_ocean.90x40x15/results_ad_nlfs
5556    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
5557      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
5558      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
5559      with SEAICE_CGRID defined.
5560    o move calendarDumps from "data" to "data.cal" and clean-up the code
5561      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
5562    o add useEXF & useCAL flags (for now, set in hard-coded way)
5563    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
5564      (were missing in NH mode, and wrong in quasihydrostatic mode).
5565      waiting for Chris updated version of calc_gw to add those CALLs.
5566    o fix bug in quasihydrostatic S/R ;
5567      add a test for this option: global_ocean.90x40x15.qshyd
5568    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
5569      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
5570    o add on/off flag useOffLine for package OFFLINE
5571    o seaice:
5572      - modify advection so that it works also on the C-grid
5573      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
5574        problem in multi-tile runs with C-grid
5575      - add flags for clipping ice velocities and/or masking solver forcing
5576      - fix drag (ocean on ice) formulation and a bug that caused noise in the
5577        C-grid solver
5578      - added a few comments to seaice_diffusion.F
5579      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
5580        are now exclusive)
5581      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
5582        required re-ordering the code a little:
5583       + make DAIRN global variable (defined in SEAICE)
5584       + move computation of the viscosities eta and zeta into a new separate
5585         routine (because I need to recompute them in seaice_ocean_stress.F)
5586    
5587    checkpoint58b_post (2006/03/13)
5588    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
5589      update output.txt of exp. aim.5l_cs.thSI
5590    o various mnc cleanups and improvements:
5591      + shrink lookup tables by factor of ~4
5592      + better error reporting when running out of lookup space
5593      + able to handle longer path/file names (up to 500 chars)
5594    o adjoint:
5595      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
5596      - TBD: "hidden" mom_vecinv recomp. in dynamics
5597    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
5598     (allow to differentiate between forcing components using new integer flags:
5599      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
5600     and add new flag to put Dissipation tendency out of Adams-Bashforth.
5601    o ecco
5602      - enable trend removal from SSH anomaly obs.
5603    o adjoint
5604      - a fix for PmEpR when #undef EXACT_CONSERV
5605      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
5606      - try to fix "hidden" recomp. in forward_step for NLFS
5607        (NLFS seems broken sometimes after I checked it in)
5608    o seaice:
5609     - add c-grid version of the dynamic solver:
5610       + three new routines that are the c-grid substitute lsr, dynsolver
5611         and ostres
5612       + put a few fields that were local to dynsolver into global common
5613         blocks, so that I can move the computation of stresses etc into
5614         seaice_lsr (saves coding but may break the adjoint).
5615     - replace more hardwired parameters by runtime parameters
5616     - add ice masks that mask the rhs of the implicit solvers where there
5617       is no ice (commented out in seaice_dynsolver, because i am not sure
5618       if this works properly), eventually this should replace the clipping
5619       of ice velocities in seaice_dynsolver to +/-40cm/s.
5620    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
5621      include it only where its needed
5622    o move balancing of fluxes before the call of external_forcing_surf
5623    o seaice:
5624      - correct units of turning angles (now they are really in degrees)
5625      - move computation of GWATX/Y out of main routine into dynsolver
5626      - initialize GWATX/Y in seaice_init
5627    o Apply mask on Fresh-Water flux (needed for SSH forcing).
5628      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
5629    o seaice: add runtime flags for turning angles (default to zero)
5630    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
5631      and trend from exf forcing and ctrl control adjustments
5632    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
5633      (since checkpoint57x_post)
5634    o change the default rotation period to 86164.s = the Earth rotation
5635    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
5636      and based on a reference stratification. Tested within hs94.cs-32x32x5.
5637    o seaice advection: add code for choosing between the default (2nd order
5638      central differences) and multiDim advection schemes provided by
5639      pkg/generic_advdiff
5640    o seaice:
5641      - removed all references to SEAICE_GRID.h fields from
5642        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
5643        (cubed-sphere configuration will change a little)
5644      - grid computations in seaice_init are obsolete now.
5645      - cleaned up code a little so that is easier to read (hopefully).
5646      - added new (better?) discretizations of default advection and diffusion
5647        (turn on with SEAICEuseFluxForm)
5648      - replace 1 in 3d global fields by kSurface in growth.F
5649      
5650    checkpoint58a_post (2006/02/13)
5651    o seaice:
5652      - bug fix in advect.F
5653    o shelfice:
5654      - separate shelfice load anomaly from pload (breaks with time
5655        dependent forcing), => introduce constant field shelficeLoadAnomaly.
5656        Its default is 0., but it may be computed more cleverly from (unknown)
5657        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
5658        done offline. A good approximation of the pressure load anomaly is
5659        necessary to avoid large initial adjustment processes underneath
5660        deep-reaching shelfice.
5661      - small fix in ISOMIP shelfice_thermodynamics
5662      - add more sophisticated thermodynamics of Hellmer (1989), this is
5663        now the default
5664      - give a few constants more intuitive names
5665    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
5666      if bulk formulae are used in long integration (especially EmPmR). Turn
5667      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
5668      if balancePrintMean, the imbalance that is substracted is printed to
5669      STDOUT.
5670    o fix bug (typo) in obcs_apply_eta.F
5671    o add a new package shelfice which enables us to model the circulation
5672      underneath shelf-ice with draughts of hundreds of meters.
5673     - works
5674     - to do: + include improved thermodynamics
5675              + check whether kSurfC (from model/inc/SURFACE.h) can be used
5676                instead of new field kTopC
5677              + can we use topoFile, Ro_surf and existing code in ini_depth.F
5678                instead of new field R_shelfIce and new code in ini_depth.F
5679                and ini_mask_etc.F?
5680              + adjust vertical mixing schemes?
5681    o seaice pkg:
5682     - add a cpp-flag to include a simple formula for a salinity dependent
5683       freezing point of sea water at the surface
5684     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
5685       meridional stresses are now different (and hopefully correct)
5686    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
5687       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
5688       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
5689    o pkg/diagnostics: add options and parameters for regional-statistics
5690       diagnostics ; define regions by reading a region-mask from a file
5691       (might add other options later)
5692    o pkg/bulk_force:
5693     - add option and parameters to use AIM surface-flux formulae.
5694     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
5695       others forcing fields (defined in PARM05, parameter file "data") are loaded
5696       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
5697     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
5698     - use the right EXCH call for uwind,vwind (to work on CS-grid).
5699     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
5700       and parameters (note: calcWindStress replaces .NOT.readwindstress).
5701     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
5702    
5703    checkpoint58 (2006/01/12)
5704    o add "--embed-source" option to genmake2 which, when the supporting
5705      tools can be compiled (as determined by genmake2) will turn on the
5706      embed_files package which then embeds the entire MITgcm source code
5707      (*.[fFhc] + Makefile) used for the build within the executable
5708      - requested by CNH but off by default
5709      - adds a paltry <9MB to the mitgcmuv executable in most cases
5710      - only writes the output when useEMBEDSRC in eedata is true
5711    o clean up 3-dim. relaxation codes:
5712      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
5713      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
5714      * Thanks to Tom Haine for testing!
5715    
5716    checkpoint57z_post (2005/12/31)
5717    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
5718      affects output (@ truncation level) of exp. plume_on_slope ; updated.
5719    o fix the pickup behavior for obcs in combination with ptracers
5720    o fix a bug in ptracers_external_fields_load
5721    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
5722      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
5723    o transfered surface NH pressure to eta field (if exactConserv).
5724    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
5725         and update lab_sea output.txt file.
5726    o completing 3-dim. relaxation code: additional term
5727         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
5728      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
5729      * At compile time, in "EXF_OPTIONS.h" set
5730          #define  ALLOW_CLIMTEMP_RELAXATION
5731          #define  ALLOW_CLIMSALT_RELAXATION
5732      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
5733          tauThetaClimRelax3Dim = 15552000.0,
5734          tauSaltClimRelax3Dim  = 15552000.0,
5735      * 3 cases:
5736          1) Use a constant-in-time 3-dim. field
5737          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
5738          3) Real-time relax. to time-evolving prescribed field
5739    o Adding Laplacian-type smoothness constraint on
5740      initial and boundary (forcing) controls (ic, bc)
5741      * enable at compile-time via
5742        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
5743      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
5744      * Absolute scale somewhat unclear so far
5745      * no area weighting was included since no other cost term does so far
5746    
5747    checkpoint57y_post (2005/12/08)
5748    First step for a NLFS adjoint
5749    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
5750    o new init. routines for calc_r_star, calc_surf_dr
5751    o still need to deal with ini_masks_etc
5752    o testreport seemed happy
5753    checkpoint57y_pre (2005/12/08)
5754    
5755    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
5756    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
5757    o add new offset feature to offline pkg (plus minor cleanup)
5758    o cfc fixes for final year of integration
5759    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
5760      be in GCHEM_OPTIONS).
5761    
5762    checkpoint57x_post (2005/12/04)
5763    o fix testreport Pb in multiple test experiment.
5764    o cleanup our namelist syntax in verification:
5765      - make it more F95 standards compliant (some work still needed)
5766      - allows the vast majority of our tests to work with gfortran
5767    o Non-Hydrostatic:
5768     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
5769     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
5770    o Allow to apply AB on T,S rather than on AB(gT,gS):
5771     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
5772     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
5773       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
5774     - need a "clever" read_pickup to restart from the other AB formulation
5775    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
5776    o remove some unused variables (reduces number of compiler warnings)
5777    o adjoint
5778      * Disable useVariableViscosity for adjoint for time being
5779        (there are a number of extensive recomputations)
5780      * Initialize certain variables needed for adjoint
5781    
5782    checkpoint57w_post (2005/11/03)
5783    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
5784                 fix the singleCpuIO RS version of MDSWRITEFIELD
5785       and add a WARNING if using globalFiles=T with multi-processors.
5786    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
5787      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
5788    o tracer advection scheme:
5789      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
5790       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
5791       was not very convenient).
5792      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
5793       (further tests needed for the implicit DST & Flux-Limiter schemes).
5794    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
5795      and sRef for convenience, handy, when you want to initialize
5796      ptracers in a large domain with a constant non-zero value. Also,
5797      untangle ptracers_init.F a little.
5798    
5799    checkpoint57v_post (2005/10/13)
5800    o change dome exp. to use variable viscosity in side-drag terms.
5801    o remove all the files from the cfc_offline test since they are now
5802      incorporated into tutorial_cfc_offline which has been producing
5803      identical results for a few days of testing
5804    o add new parameter: sideDragFactor to enable half-slip-side BC
5805      and change side-drag S/R to use viscosity from mom_calc_visc
5806      (can switch back by setting sideDragFactor=0.); affects results at
5807      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
5808       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
5809    o vorticity & strain are now computed without masking, to account for
5810      no-slip-side BC in variable viscosity calculation ; mask is applied
5811      anyway later on, before computing advection/coriolis terms.
5812    o modify exp4 to test new obcs support for reading from external files
5813      and for passive tracers
5814    o fix behavior of ptracers_monitor when monitor output is written to a
5815      netcdf-file; still not independent of monitor.F (writes in the same
5816      file).
5817    o change default value of tRef (put a uniform, meaningful value for ocean
5818      & atmos) and initialize sRef (was missing, as Martin mentioned).
5819    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
5820      to be proportional to enstrophy dissipation length.  Thus,
5821       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
5822      This is now consistent with Smagorinsky and with the manual.
5823    
5824    checkpoint57u_post
5825    o OBCS and PTRACERS: add open boundary support for passive tracers
5826      - either use homogenous (pseudo) v.Neumann conditions or prescribe
5827        OB-values from file; this is not different from the way theta and salinity
5828        are treated
5829      - however, Orlanski-radiation conditions are not supported, and the model
5830        will stop if you use pTracers and Orlanski at the same time.
5831      - beefed up the rountine obcs_external_fields_load: now only those open
5832        boundary values are overwritten with values from files for which there
5833        are really files, otherwise the OB-fields remain untouched. This makes
5834        it possible to use different OBs at different ends of the domain (as
5835        with EXF)
5836    o reduce number of exch calls in shap_filt (s2).
5837    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
5838      truncation level) 4/5 MLAdjust test results (11&12 digits match).
5839    
5840    checkpoint57t_post (2005/10/03)
5841    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
5842    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
5843      same truncation, independent of the face number: affects affects several
5844      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
5845    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
5846      note that biharmonic viscosity + no-slip was not tested in any experiment.
5847    o fix bug in non-linear free-surf side-drag ; generate new output for
5848      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
5849    o make mnc honor the writeBinaryPrec flag for most kinds of output
5850    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
5851    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
5852      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
5853    o add brackets in multi-terms sum to get same truncation, independent of
5854      the face number (manage to get exactly same value of gU,gV at the cs-edge)
5855      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
5856    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
5857      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
5858      a maximum grid-scale Reynolds number.  Also, changes all length calculations
5859      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
5860      Suggested values of viscosity parameters found in mom_calc_visc.
5861      Many new viscosity diagnostics available.
5862    
5863    checkpoint57s_post (2005/09/20)
5864    o Add clearing-house for viscosity calculations, mom_calc_visc and
5865      correct numerous bugs in LeithD and Smagorinsky discretizations.  
5866      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
5867      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
5868      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
5869      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
5870      The Strain-Tension form is now called with useStrainTensonVisc=.true.
5871      ViscAhStrain and viscAhTension are now retired.
5872    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
5873    o In response to JMC's bug report, genmake2 now ignores any soft-links
5874      that it finds in the *current* directory when searching for files.
5875      Soft-links found in any other source directories will still work as
5876      they did before.
5877    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
5878      a C routine to unlimit the stack size
5879    o mnc-ify pkg/aim snapshot vars
5880    o mnc-ify pkg/land as requested by Daniel
5881    o various changes to mnc including:
5882      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
5883      - output can now be grouped so that all files within a group
5884          change the ITER portion of their names in lock-step together
5885      - can now read ("global") PER-FACE (in addition to PER-TILE) files
5886          and works with both EXCH1 and EXCH2 (but needs more testing)
5887      - writing works for all verification test cases w/ g77 on Linux
5888    
5889    checkpoint57r_post (2005/09/07)
5890    o make MNC variable initialization happen earlier
5891    o add diagnostics for (almost) each term of the momentum Eq.
5892    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
5893    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
5894    o remove MINIMAL_TAVE_OUTPUT option ;
5895      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
5896    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
5897      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
5898    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
5899    o add time-dependent SST, SSS control
5900    o cost terms in ecco/ modularized (new cost_generic.F)
5901    o cost_averages routines are modularized (new cost_averagesgeneric.F)
5902    o new infrastructure for seaice model vs. obs misfits in seaice/
5903      * driver from the_main_loop.F is seaice_cost_driver.F
5904      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
5905      * gradient check in Exp. 6a of natl_box_adjoint/
5906    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
5907      (see README file)
5908    
5909    checkpoint57q_post (2005/08/19)
5910    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
5911    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
5912      - bug was reported by Jean-Michel and Ian Fenty
5913    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
5914      update exp. cpl_aim+ocn output.
5915    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
5916      Needed for high-res. runs with large global files
5917      to be able to limit tapelev size
5918    o Changed some tests for adjoint:
5919      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
5920      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
5921      * global_ocean.90x40x15/ back to default 3-level checkpointing
5922    o Modifications to enable scripted COMMON to MODULE conversion
5923      * verification/OpenAD/code/ has necessary scripts and description;
5924      * converts, compiles and runs successfully;
5925    
5926    checkpoint57p_post (2005/08/01)
5927    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
5928    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
5929      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
5930    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
5931    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
5932      (was already the case for dissipation with mom_vecinv,
5933       and also the case for grad.PhiHyd when staggered-timeStep)
5934      This will allow to put dissipation out-off the AB time-stepping.
5935     Unfortunately, affects truncation error. Update output of exp. that "fails"
5936      (cg2d matching number) and leave the others for later: front_relax(10),
5937      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
5938      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
5939    
5940    checkpoint57o_post (2005/07/30)
5941    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
5942      (2) its ready to be documented during the 20050801 DocFest
5943    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
5944      for ideal_2D_oce and lab_sea on linux_ia32_g77
5945    o set to #undef CTRL_SET_OLD_MAXCVARS_30
5946      in global1x1_tot/code_seaice_adj to access indices 32, 33
5947      (worth another tag)
5948    
5949    checkpoint57n_post (2005/07/29)
5950    o adding precip control xx_precip 32
5951    o adding swflux control xx_swflux 33
5952    o Replacing 10 forcing penalty cost routines by 1 generic.
5953    o Implementing partitioning in time-mean and variable adjustment
5954      for atmos. state.
5955    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
5956    o in natl_box_adjoint:
5957      * updated exp 1 to 10
5958        (but does not have time-mean vs. variable split results yet)
5959    o updated global1x1/*_seaice_adj/
5960      to incorporate latest changes
5961    o enable useSingleCpuIO for mdsio vector routines
5962      (applies in particular to tapelev I/O)
5963    o removed inefficient K-loop in all active_file*control*.F
5964    
5965    checkpoint57m_post (2005/07/28)
5966    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
5967      and advect_cs (use EXCH-2 and standard cs-32 grid files).
5968    o pkg/exch2: filling of face-corner halo regions is optional
5969      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
5970    
5971    checkpoint57l_post (2005/07/14)
5972     tag before updating tutorials (pre-release-2)
5973    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
5974       for output and interpolation of input fields onto model grid)
5975    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
5976       Affects results of exp. rotating_tank ; update output.txt.
5977    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
5978          and taking the square quantity and/or using a fraction-weight field.
5979    o fix aim_diagnostics_init.F mate numbers.
5980    o add mnc output capability to diagnostics/diagstat and update
5981      our cvsignore files for the ACSII output generated
5982    
5983    checkpoint57k_post (2005/07/02)
5984    o lab_sea now uses diagnostics package and provides a suite of
5985      new EXF diagnostics output.
5986    
5987    checkpoint57j_post (2005/06/30)
5988    o exf
5989      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
5990        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
5991        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
5992      * extended diagnostics output
5993        - now includes all EXF variables
5994        - hs, hl moved to common block
5995        - separate S/R for diagnostics, called after ctrl vector is added
5996        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
5997        - EXFqnet contains true Qnet (i.e. includes qsw)
5998      * updated verif. lab_sea, global_with_exf
5999      * Rearranging hflux (exf_mapfields -> exf_getforcing)
6000        to ensure that diagnostics sees a true EXFqnet
6001    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
6002    o diagnostics pkg: change pointers so that 1 diagnostic can be used
6003      several times with different frequencies.
6004    o mnc-ify the thsice package as requested by Daniel Enderton
6005      - the monitor--MNC output needs work
6006      - many attributes need to be added (most are currently blank)
6007    o mnc-ify theaim_v23 package as requested by Daniel Enderton
6008      - many attributes need to be added (most are currently blank)
6009    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
6010    o add Sadourny like discretization to the 4th.O vorticity advection scheme
6011    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
6012      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
6013         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
6014    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
6015     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
6016    
6017    checkpoint57i_post (2005/06/19)
6018    o Diagnostics package was changed: diagnostic allocation is now deactivated
6019      by setting an empty file name in the namelist (used to be by setting 0 frequency)
6020    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
6021      add 1rst Order upwind vertical Shear.
6022    o add a quick fix for A/B checkpointing in OFFLINE mode
6023    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
6024      end-run around the C/Fortran linking horror in eesup/src/timers.F
6025    o added pkg/runclock: allows user to terminate run based on wall clock
6026    o added non-hydrostatic scaling parameter: nh_am2
6027    o pkg/my82: futile attempt to make results compiler-independent by adding
6028      some "_d 0", etc. no effect.
6029    o for mnc output, fill the 'T' coordinate var with myTime and create a
6030      separate 'iter' variable for iteration count
6031    o pkg/diagnostics:
6032      add new capability: output of Global/Regional & per-level statistics ;
6033      tested against monitor output (including land & thSIce) on various exp.
6034    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
6035    
6036    checkpoint57h_done (2005/05/19)
6037      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
6038      data.diagnostics, data.gchem, data.ptracers) is done.
6039    
6040    o pkg/diagnostics: prepare for Global/Regional statistics.
6041      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
6042    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
6043      and rename it: DIFFERENT_MULTIPLE
6044    
6045    checkpoint57h_post (2005/05/14)
6046    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
6047    o pkg/diagnostics: change output frequency, now in seconds (instead
6048      of Nb of iterations). This requires to change data.diagnostics.
6049    checkpoint57h_pre (2005/05/12)
6050    
6051    o in mnc, let the user create the output dir if both mnc_outdir_date
6052      and mnc_outdir_num are false
6053    o add fflags() to pkg/diagnostics which allows one to specify, on a
6054      per-file basis, the file precision [default behavior is unchanged]
6055    o added diagnostics to pkg/kpp, including computation of mixed layer
6056      depth based on a temperature/density criterion
6057    o updated verification/natl_box to test the new pkg/kpp diagnostics
6058    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
6059    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
6060    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
6061      not mnc -- this mistake was found by JMC and is now corrected
6062    
6063    checkpoint57g_post (2005/04/15)
6064    o add Adams-Bashforth 3rd Order time stepping:
6065      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
6066      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
6067    checkpoint57g_pre (2005/04/15)
6068    
6069    o make lambda[Theta,Salt]ClimRelax spatially varying
6070      (default remains spatially uniform constant based on tau)
6071    o added new control variables
6072      * init. uVel, vVel, etanN
6073      * lambda[Theta,Salt]ClimRelax
6074    o separate masks used for ctrl_pack/unpack 'from write_grid' output
6075      (suggested by G. Forget)
6076    
6077    checkpoint57f_post (2005/04/06)
6078    o add parameter "baseTime" = model base time = time at iteration zero
6079      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
6080      account for baseTime shift
6081    o move Coriolis arrays from PARAMS.h to GRID.h
6082    checkpoint57f_pre (2005/04/06)
6083    
6084    o mnc-ifying the seaice package
6085    o introduced an alternative length scale calculation for use in the limiting
6086      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
6087    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
6088    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
6089      as well as grad(vort3).  Made it compatible with both approximate form
6090      for the cubed sphere and full form of these gradients.  Added flag
6091      useFullLeith to select between approximate and full form.  
6092    o add "d0" in getcon.F to reduce differences between compilers/platforms
6093      update output.txt of exp. fizhi-gridalt-hs
6094    o change port_rand funtion to allow to set the seed.
6095    o fix obscure MNC bug involving conversion between reals and integers
6096      - it caused no problems with certain (eg. gcc, ifc) compilers but the
6097        new version is now more standards-compliant
6098    o adjoint-related modifications
6099      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
6100      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
6101      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
6102    
6103    checkpoint57e_post (2005/02/28)
6104    o Adding eddy stress controls a la Ferreira et al.
6105    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
6106    
6107    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
6108      update output.txt of exp. fizhi-gridalt-hs
6109    o add more "Z" dimensions and associated coordinate vars to MNC
6110    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
6111    o parameter calendarDumps: when set, approximate months (30-31 days) and years
6112      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
6113      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
6114      months and years.  Requires pkg/cal.
6115    o diagnostics: add pickup functionality
6116      - off by default for backwards compatibility
6117      - current version only uses MDSIO -- MNC will be added
6118    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
6119    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
6120    
6121    checkpoint57d_post (2005/02/11)
6122    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
6123    o modify verification/ideal_2D_oce so that it tests the creation of mnc
6124      output from the diagnostics package
6125    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
6126    o make genmake2 more portable by using ".$FS" instead of ".f" for more
6127      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
6128    o add coordinate variables to the MNC output from the diagnostics package
6129    o change MNC-flags default value: true when useMNC=TRUE
6130    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
6131      the ability (off by default) to read the grid information using MNC
6132    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
6133    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
6134    o do snap-shot diagnostics at the middle of the time-interval (instead of
6135      at the end).
6136    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
6137      new test for AIM with thSIce + slab-ocean
6138    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
6139    o move state variable diagnostics to the beginning of the time step ;
6140      (note: still needs some work specially for snap-shot diagnostics)
6141      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
6142    
6143    checkpoint57c_post (2005/01/27)
6144    o Change testing option (-ieee) to get closer agreement between g77 & ifort
6145    o generate new output.txt files on faulks with g77 & the new -ieee option
6146    checkpoint57c_pre (2005/01/27)
6147    
6148    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
6149      update output.txt of exp. global_ocean.90x40x15
6150    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
6151      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
6152    o add saltFlux(+File) forcing capability with periodicExternalForcing
6153    o allow to use pkg diagnostics for GM-Redi & ThSIce output
6154    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
6155    o improvements for the MNC output from DIAGNOSTICS:
6156      - correct handling of the unlimitied dimension
6157      - all dims now have associated coordinate variables
6158      - variables located at U, V, and Corner ("Z") points are now written
6159        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
6160        *all* data points are output
6161    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
6162    o added pkg/seaice/seaice_monitor.F
6163    o mdsio_readfield.F can now read files visible only to master MPI process.
6164    o pkg/seaice: some test code for ice-modified ocean stress
6165    o exf_getffields interpolation defaults to bilinear for all scalar forcing
6166      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
6167      spurious negative numbers for precipitation and humidity.  Will cause
6168      some small numerical differences for integrations using pkg/exf/exf_interp.F.
6169    o pkg/ctrl/
6170      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
6171        May be enabled via doPackDiag
6172      *  introduce z-scaling of
6173         + gradient (doZscalePack) and
6174         + control (doZscaleUnpack)
6175    o pkg/mdsio/
6176      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
6177      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
6178    
6179    checkpoint57b_post (2004/12/20)
6180    o simplify options in diagnostics_fill arguments (remove weird combinations)
6181    o fix MNC coordinate variables so that they now contain per-face index
6182      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
6183      general, EXCH2 grids are only aligned to a "local" coordinate system
6184    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
6185    o Implement instantaneous output within pkg diagnostics:
6186      setting a negative frequency in data.diagnostics produces
6187     "snap-shot" output (as opposed to time-average if freq > 0)
6188    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
6189      NOTE: change ptracer diagnostics name: use 2 characters to work with
6190            more than 9 tracers. Add also diagnostics of advect & diffus flux.
6191    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
6192      becomes the coordinate variable for the 'T' dimension
6193    o add CF-style coordinate variables to MNC
6194      - just a first cut:  numbers are meaningless on the cubesphere and
6195        missing along the T axis but otherwise it works!
6196    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
6197    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
6198    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
6199      this is based directly on what the model compute, so that the content of
6200      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
6201    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
6202    o clean up build options files for SunOS, in particular
6203      - remove -traditional from xmakedepend
6204      - change -xarch=v9 to -xarch=native for f77
6205      - restore use of make (not gmake)
6206      - add CC=gcc if using g77
6207    o changes per discussion of AM, JMC, & EH3 today:
6208      - move redundant "grid" variables out of "state" -- in preparation of
6209        creating proper CF-style coordinate variables and in recognition
6210        that any/all grid variables can be easily copied (eg. w/NCO) from
6211        the grid files into any of the other NetCDF files
6212      - *always* output grid variables with MDSIO (this will eventually be
6213        changed)
6214      - output MNC grid file if useMNC is true
6215    o every instance of _END_MASTER() has been found and replaced with
6216      _END_MASTER( myThid ) in order to satisfy certain picky Sun
6217      preprocessors
6218    o re-arrange diagnostics pkg initialisation:
6219     - allow each package to extend the available diagnostics list
6220     - add some checking and fix small problems (multi-threaded, ...)
6221     - new S/R diagnostics_fill (replace fill_diagnostics):
6222       look through the short list of active diag. (instead of the long list)
6223       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
6224    
6225    checkpoint57a_post (2004/12/10)
6226    o this set of changes restores TAMC compatibility
6227      tested for global_ocean.90x40x15 adjoint on trough
6228      (what a pain)
6229    
6230    checkpoint57a_pre (2004/12/10)
6231    o some modifs in tools/build_options for sunos
6232    o call ctrl_pack for ctrl at end for optimcycle=0
6233    
6234    checkpoint57 (2004/12/09)
6235    o add horizontal bi-harmonic viscosity for vertical velocity
6236      - new parameter viscA4W (defaults to viscA4)
6237      - affects only non-hydrostatic code
6238      - to be done: no-slip lateral boundary conditions
6239    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
6240    o implement Implicit Vertical advection for pTracers
6241    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
6242      (implemented also for implicit vertical diffusion & advection)
6243    o OBCS: extend application of tracer open boundary conditions
6244      to a strip beyond the boundary of width Olx/Oly
6245    o add call monitor to TAF set of required calls (flow directives)
6246      and include in natl_box_adjoint
6247    o untangle a few ifdefs related to cost, ctrl, autodiff
6248      untangel a few ALLOW_ECCO_OPTIMIZATION
6249    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
6250      (theta2, salt2 in ecco_cost_weights)
6251    
6252    checkpoint56c_post (2004/12/03)
6253    o OBCS as control variables
6254      - update ctrl_ad_diff.list, obcs_ad_diff.list
6255      - remove balance of obcs controls from default
6256      - fix index bug nobcs in ctrl_init
6257      - fix dummy fields filen in ctrl_pack
6258      - add dummy weights for obcs
6259    o lsopt: comment out fort.94 output
6260    o optim:
6261      - remove unnecessary header files
6262      - adjusted namelists
6263      - add xerbla.F to Makefile
6264    o exf:
6265      - multiple modifications of exf_check_range
6266      - unit change in exf_init_runoff from [m/year] to [m/s]
6267    o mdsio:
6268      - i/o-vector change debugLevel from debLevA to debLevB
6269    
6270    checkpoint56b_post (2004/12/01)
6271    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
6272      is called from DO_THE_MODEL_IO
6273      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
6274      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
6275      - clean up PTRACERS_WRITE_TIMEAVE a little
6276    o add another verification experiment that tests both the cfc-pkg and
6277      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
6278      reactive tendencies treated inline with regular timestepping
6279    o testreport previously did a lousy job of comparing small numbers, so
6280      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
6281      implemented in the little c-progam tmp_cmpnum.c which is embedded in
6282      testreport.
6283    o ptracers_monitor: bug fix for MPI
6284    
6285    checkpoint56a_post (2004/11/28)
6286    o GCHEM: finish reorganizating the package
6287      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
6288        (introduces another 3D-array for each passive tracer, but only if
6289        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
6290        gchemTendency is not needed because the timestep is done separately)
6291      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
6292      - GCHEM is now---more or less cleanly---separate from PTRACERS
6293      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
6294        so clear to me how that should be done in a general way.
6295    o CFC: improve formatting of output in CFC_ATMOS
6296    o PTRACERS:
6297      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
6298        that ALL experiments with ptracers enable can be checked. This makes
6299        GCHEM_MONITOR obsolete.
6300      - include a runtime parameter PTRACERS_monitorFreq that defaults to
6301        monitorFreq
6302      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
6303    o add PTRACERS (PTR0[1-5]) to testreport output
6304    o exf_check_range:
6305      * default changed to .TRUE.
6306      * will check values for niter0 if debLevA, every timestep if debLevB
6307      * STOP in exf_check_range if 'out of range'
6308      * range chosen generous to allow for potential extema
6309      TBD: a version with stricter range
6310           permitted range would be runtime parameters
6311    o GMredi:
6312      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
6313      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
6314      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
6315    o GCHEM:
6316      - move call to GCHEM_FORCING_SEP, so that it is now called before
6317        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
6318      - introduced a useGCHEM runtime flag and applied it everywhere.
6319      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
6320        this flag is now only visible within GCHEM-pkg routines.
6321      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
6322        be replaced by a 3D array that is computed before thermodynamics; for
6323        this, the tracer ID iTracer had to be included into the parameter list
6324        of ptracers_forcing
6325      - set up forward_step to call gchem_forcing, that will replace
6326        gchem_forcing_int in ptracers_forcing
6327      - cleaning up
6328    o small cleaning of exch2: remove files that are also in eesupp/src
6329    
6330    checkpoint56 (2004/11/17)
6331    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
6332    o mnc: cleanup "full" files--fixes out-of-memory problem
6333    o ECCO-GODAE
6334      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
6335      * fully merged and updated from SIO code
6336        windstress sign change affects
6337        - exf_inscal_[u/v]stress
6338        - sign of xx_tau[u/v] adjustments
6339        - signs in cost_scat
6340      * ctrl_get_gen: avoid update of tau[u/v] for first few days
6341      * natl_box_adjoint updated and compressed
6342      * 2-level checkpoint switch added
6343        (tested in EXP. 1 of natl_box_adjoint)
6344      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
6345    o SVD
6346      * first complete, non-hacked version for SVD calculations
6347      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
6348        performed via direct access files admtlm_vector.it????
6349        (via ctrl_[un]pack)
6350      * optimcycle is used for ARPACK iteration counter
6351        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
6352      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
6353        and add linear transforms where necessary
6354      * controls are initial/final SST, SSS (can be extended; need to check
6355        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
6356    o mdsio: filename info to both stderr, stdout
6357    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
6358      from sign change
6359    
6360    checkpoint55j_post (2004/11/10)
6361    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
6362      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
6363    o add consistent build directories and .cvsignore files to verification
6364    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
6365    o make all subroutines 30 or less characters in length for certain older
6366      compilers to work (a thorough search only turns up two routines in
6367      pkg/ptracers)
6368    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
6369      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
6370    
6371    checkpoint55i_post (2004/10/28)
6372    o change arrays for total vertical diffusivity (2.D if explicit,
6373      3.D if implicit) ; each ptracer uses its own background value.
6374    o added mnc/NetCDF output capability to ocn_compon_interf
6375      - added bits to verification/cpl_aim+ocn so that it can run on
6376        ITRDA and other clusters without the mpirun "-wd" option
6377    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
6378      configuration
6379    o give MNC the ability to create additional files rather than
6380      exceeding a specified file size limit "MNC_MAX_FILESIZE"
6381      - the default is just less than 2GB which is a practical limit
6382        on many systems
6383    o Compute the non-local term using either KPP vertical diffusivity (=default)
6384       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
6385    
6386    checkpoint55h_post (2004/10/20)
6387    o add verification test "vermix"
6388    o remove all the *_ioinc flags and replace with the single global
6389      outputTypesInclusive flag
6390    o allow to set a vertical profile of vertical diffusivity for T & S
6391    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
6392    o useMNC moved from data.mnc to data.pkg
6393    
6394    checkpoint55g_post (2004/10/14)
6395    o Renaming carbon AD experiments to comply with testreport conventions
6396    o Updating adjoint of Held-Suarez hs94.1x64x5
6397    o Fixing directives for non-ECCO forward_step, after ECCO directives
6398      have been fixed to avoid recomp. of do_oceanic_phys
6399      Works well for global_ocean.90x40x15,
6400      but recomp. issue remains for carbon
6401    o Updating adjoint output for natl_box_adjoint after
6402      pkg/ecco has been modified (see taga c55d_post)
6403    
6404    checkpoint55f_post (2004/10/13)
6405    o rename to timeave_init_fixed
6406    
6407    checkpoint55e_post (2004/10/13)
6408    o some delicate re-shuffle of store directives to avoid one
6409      extra call of do_oceanic_physics
6410      affects ecco_the_main_loop.F, do_oceanic_physics.F
6411      checkpoint_lev1_directives.h
6412    o NB: this may break global_ocean adjoint temporarily,
6413      but it is clear how to fix it. Will do later, need this now.
6414    
6415    checkpoint55d_post (2004/10/11)
6416    o ECCO specific cost function terms (up-to-date with 1x1 runs)
6417    o ecco_cost_weights is modified to 1x1 runs
6418    o modifs to allow observations to be read in as
6419      single file or yearly files
6420    o enable to read exf forcing fields as either
6421      single file or yearly files (flag useExfYearlyFields)
6422    checkpoint55d_pre (2004/10/08)
6423    
6424    o switch between 2-level and 3-level checkpointing
6425    o add ability of MNC to write local and "partial" (eg. 2D slices where
6426      the full 3D field is never actually stored) arrays to NetCDF files
6427      with the correct (that is, the complete multi-dimensional) set of
6428      array indicies
6429      - used in mom_vecinv() to write the diagFreq output
6430      - tested (demonstrated) in verification/aim.5l_cs
6431    o further mnc-ification
6432      - add verification/lab_sea to the list with mnc setups
6433      - fix undefined mnc v-names in cd_code
6434      - add kpp to mnc output (both snapshot and timeave)
6435    o non-hydrostatic code
6436      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
6437        in calc_gw.F
6438      - defaults to viscAh
6439      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
6440        friction or Leith) in non-hydrostatic mode, as long as there is
6441        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
6442    o pkg/cost
6443      extend simple cost functions to treat time mean quantities
6444      (T,U,V) via cost_accumulate_state from cost_tile
6445    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
6446        be 2 times larger than the minimum size the advection scheme requires.
6447        now get a perfect conservation of salt in advect_cs test-exp (updated)
6448    o GGL90 (Gaspar's TKE mixed layer)
6449      - add horizontal diffusion of TKE, requires exchanges in
6450        do_fields_blocking_exchanges, horizontal diffusivity is zero by
6451        default. In OPA there is no horizontal diffusion of TKE but the
6452        mixing coefficients are computed from a horizontal average of TKE of
6453        6 points or so. I think that diffusion has a little more physical
6454        justification.
6455      - clean up ggl90_calc in the hope of reducing memory usage (this hope
6456        was in vain)
6457      - mask tke-variable in ggl90_init
6458    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
6459    o fix biharmonic diffusion on CS-grid.
6460    o more obcs stuff
6461      - added obcs_external_fields_load as an alternative to the EXF-pkg option
6462        for reading boundary values. This routine is called from
6463        obcs_prescribe_read
6464      - updated obcs_check
6465      - changed sponge layer relaxation parameter units for days to seconds
6466      - turned off sponge layer by default
6467      - changed argument list of OBCS_CALC to myTime+deltaTclock
6468      - fixed about 35 bugs in obcs_external_fields_load
6469    
6470    checkpoint55c_post (2004/09/23)
6471    o obcs stuff
6472      - new runtime flags useOBCSprescribe, useOBCSbalance
6473      - re-arranged obcs_calc
6474      - moved exf_getobcs to obcs_prescibe_read
6475        obcs_prescibe_read is called after ORLANSKI stuff
6476        and independent of it (executable can contain all).
6477      - updated obcs_check
6478      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
6479        These may be necessary only if tangential velocities are
6480        prescribed at OB, not sure, needs testing.
6481    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
6482      which simplifies the calls and passes the ifc check-bounds test
6483    
6484    checkpoint55b_post (2004/09/22)
6485    o add a 2D scalar, Z location, exchange_2 routine.
6486    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
6487      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
6488      affects advect_cs results (for the wrong reason): update output.txt
6489    o use a more standard discretization for biharmonic viscosity ;
6490     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
6491      affects results of dome set-up: update output.txt
6492    o fix gad_advection.F (CubedSphere part), back to version 1.23
6493    o fix bug in mom_vi_del2uv.F (CubedSphere part).
6494    
6495    checkpoint55a_post (2004/09/20)
6496    o merged code to
6497      * prescribe/read time-dependent open boundaries
6498        (works in conjunction with exf, cal)
6499      * sponge layer code for open boundaries
6500      * each boundary N/S/E/W now has its own CPP option
6501        (healthy for the adjoint)
6502    
6503    checkpoint55 (2004/09/17)
6504    o up-to-date adjoint of previous breaks
6505      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
6506      - global_ocean_ebm: adjoint still needs fix (TLM ok)
6507      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
6508      - carbon: * remove tr1-related adjoint verification
6509                * add ptracer as control variable
6510    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
6511      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
6512    
6513    checkpoint54f_post (2004/09/16)
6514    o in verification/carbin/ remove experiment related to
6515      ALLOW_PASSIVE_TRACER (array tr1 etc)
6516      code_ad/ input_ad/ results_ad
6517    
6518    o add two new packages
6519      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
6520        + subject to optimization (memory)
6521      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
6522        + subject to reordering (many GOTOs in the original code)
6523        + so far opps is called for every (i,j) point, and then operates in
6524          the vertical; one may want to reorder the scheme in order operate in
6525          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
6526          fields)
6527    o overhaul of IO so that we now have flags for MDSIO and/or MNC
6528      - all verification tests compile and run with linux_ia32_g77
6529      - defaults are compatible with current input files--nothing
6530        should change if you were not previously using MNC
6531      - MNC output has been added in numerous places (eg. timeave)
6532        but there are still a few writes not yet do-able with MNC
6533        (this is in progress)
6534      - flags now allow for either/or/both use of MDSIO and MNC and
6535        documentation will soon follow
6536      - numerous small formatting cleanups for ProTeX
6537    o add version info (via BUILD_INFO.h) to MNC and stdout
6538    
6539    checkpoint54e_post (2004/09/02)
6540    o add two new packages
6541      - pp81 (Packanowski and Philander, 1981), Richardson number and
6542        stratification dependent mixing
6543      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
6544      - these scheme operate in a similar manner as KPP (without ghat, of
6545        course), however there is only one diffusivity that is used for both
6546        temperature and salinity (and passive tracers)
6547    o add offline package
6548    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
6549      provided by Stephanie Dutkiewicz
6550    o genmake2: add ability to search for C compilers and cleanup test output
6551      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
6552    
6553    checkpoint54d_post (2004/07/27)
6554    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
6555    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
6556      leading to additional shift by 5 days each year of integration
6557       (i.e. leading to considerable offset over the years)
6558    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
6559    o start with no AB and no initial filtering (staggerTimeStep):
6560      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
6561    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
6562      (external loading & cpl import/export stay in forward_step.F)
6563    o update coupling interface to work with new staggerTimeStep
6564    o change MDSIO ptracers_pickup.
6565    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
6566    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
6567    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
6568    
6569    checkpoint54c_post (2004/07/18)
6570    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
6571      this affects (truncation error) output.txt of test-exp:
6572       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
6573    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
6574    o change Qnet to always be the net heat flux, (+upward).
6575      affects (truncation error) output of natl_box exp.: updated
6576    o define the max number of passive tracers in PTRACERS_SIZE.h
6577    o start to test mnc routinely in exp0
6578    o add sea-ice loading (sIceLoad) as a new forcing field.
6579    
6580    checkpoint54b_post (2004/07/08)
6581    o add testreport "-j JOBS" option for parallel builds (tested and pretty
6582       impressive on Altix and Opteron systems)
6583    o diagnostics can now write NetCDF files through the mnc package
6584    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
6585    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
6586    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
6587      affects (truncation error) output of lab_sea & natl_box exp.: updated
6588    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
6589    
6590    checkpoint54a_post (2004/07/06)
6591    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
6592    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
6593    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
6594    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
6595      + internal_wave (shift in writing cg2d_ini_res)
6596    checkpoint54a_pre (2004/07/05)
6597    
6598    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
6599      - modified verification/lab_sea and natl_box_adjoint accordingly
6600    
6601    checkpoint54 (2004/07/02)
6602    checkpoint53g_post (2004/07/02)
6603    o prepare splitting of thermodynamics: store convect.counter in common block
6604    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
6605      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
6606    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
6607    o new parameter "nShapS": allow to treat differently S from T (nShapT)
6608    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
6609    o restore adjointability
6610    
6611    checkpoint53f_post (2004/06/25)
6612    o modifications that affect AIM experiment results (update output.txt):
6613      - no advection of S at top interface Nr (pkg/generic_advdiff)
6614      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
6615    o AIM pkg:
6616      - include stability function into surf.Flux derivative relative to Tsurf
6617      - calculate clear-sky radiation & surface temp. change (for diagnostics)
6618    
6619    checkpoint53e_post
6620    o merged cylindrical coord configuration
6621    o added rotating_tank experiment
6622    checkpoint53e_pre
6623    
6624    checkpoint53d_post (2004/06/14)
6625    o faulks upgraded: re-generate output.txt that have changed:
6626       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
6627    o Added Bryan and Lewis, 1979, vertical diffusivity profile
6628    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
6629    o added Sadourny discretization of Coriolis
6630      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
6631      - re-enabled use of omega3 (useAbsVorticity)
6632    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
6633      vector-invariant equations
6634      - note: does *NOT* yet use same variable visc. for no-slip BC's.
6635    o recoded the lateral boundary conditions for non-hydrostatic w, this time
6636      hopefully without new bugs
6637      - still to do: biharmonic friction for non-hydrostatic w
6638    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
6639    o regenerated output for global_ocean_ebm (using -ieee)
6640    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
6641      of mom_common/
6642      - simple re-arrangement of instructions within computing loop
6643    checkpoint53d_pre (2004/05/21)
6644    
6645    checkpoint53c_post (2004/05/21)
6646    o new version of coupler for AIM+thSIce and Ocean models
6647     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
6648     - land: change Evaporation of snow
6649     - aim with thSIce: fix bug in snow-precip.
6650  o changes to calc_gw.F  o changes to calc_gw.F
6651   - bug fix for w^2 term near the bottom boundary   - bug fix for w^2 term near the bottom boundary
6652   - (hopefully) improve the lateral slip boundary condtions for use with   - (hopefully) improve the lateral slip boundary condtions for use with
# Line 10  o changes to calc_gw.F Line 6654  o changes to calc_gw.F
6654    - because the bug fix changes two verification experiments anyway (exp5    - because the bug fix changes two verification experiments anyway (exp5
6655      and plume on slope), change the lateral boundary condition from half slip      and plume on slope), change the lateral boundary condition from half slip
6656      to the value of no_slip_sides      to the value of no_slip_sides
6657    o ebm package wasnt quite up to the parallel task. Fixed that.
6658    o Adjoint of EBM package + verification
6659      * TLM OK
6660      * ADM not sufficient accuracy yet (needs further testing)
6661    
6662  checkpoint53b_post  checkpoint53b_post (2004/05/14)
6663  o Commiting new energy balance model to repository  o Commiting new energy balance model to repository
6664    * package is pkg/ebm    * package is pkg/ebm
6665    * verif. is verification/global_ocean_ebm    * verif. is verification/global_ocean_ebm
# Line 29  C        Destabilization of the thermoha Line 6677  C        Destabilization of the thermoha
6677  C        by atmospheric eddy transports.  C        by atmospheric eddy transports.
6678  C        J. Climate 7(12), 1870-1882  C        J. Climate 7(12), 1870-1882
6679  o Will need long integration testing.  o Will need long integration testing.
6680  checkpoint53b_pre  checkpoint53b_pre (2004/05/14)
6681    
6682  o created pkg/mom_common in preparation for variable viscosity code  o created pkg/mom_common in preparation for variable viscosity code
6683  o renamed and split ini_mnc_io  o renamed and split ini_mnc_io
# Line 37  o pkg/land: only liquid water can diffus Line 6685  o pkg/land: only liquid water can diffus
6685  o AIM using land: soil wetness availability account for snow  o AIM using land: soil wetness availability account for snow
6686  o added printMapIncludesZeros to EEPARMS namelist  o added printMapIncludesZeros to EEPARMS namelist
6687    
6688  checkpoint53a_post  checkpoint53a_post (2004/05/11)
6689  o restore TAMC compatiility for exf_constants.h  o restore TAMC compatiility for exf_constants.h
6690    (no usage of _d in .h)    (no usage of _d in .h)
6691  o Additional storing in KPP in an attempt to fix  o Additional storing in KPP in an attempt to fix
# Line 50  o Fixed verification/natl_box_adjoint ex Line 6698  o Fixed verification/natl_box_adjoint ex
6698    and hence gives results closer to that of Experiment 2.    and hence gives results closer to that of Experiment 2.
6699    Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.    Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
6700    
6701  checkpoint53  checkpoint53 (2004/05/06)
6702  o stable checkpoint with up to date adjoint  o stable checkpoint with up to date adjoint
6703    TLM tests only run for 1st grdchk at the moment. Its unclear if    TLM tests only run for 1st grdchk at the moment. Its unclear if
6704    this is a code problem or a problem with resetting code for g_    this is a code problem or a problem with resetting code for g_
# Line 60  o stable checkpoint with up to date adjo Line 6708  o stable checkpoint with up to date adjo
6708     o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)     o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
6709       are both still in chaos following their security messes.       are both still in chaos following their security messes.
6710    
6711  checkpoint52n_post  checkpoint52n_post (2004/05/06)
6712  o various build (mostly genmake2) changes including:  o various build (mostly genmake2) changes including:
6713    - ability to build/run more easily within Cygwin and MacOS X    - ability to build/run more easily within Cygwin and MacOS X
6714    - more complicated Makefiles with a stronger dependence on Gnu Make    - more complicated Makefiles with a stronger dependence on Gnu Make
# Line 91  o fix in pkg/thsice: Line 6739  o fix in pkg/thsice:
6739    - maintain snow precipitation unchanged (even if Tsf >=0).    - maintain snow precipitation unchanged (even if Tsf >=0).
6740   both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice   both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
6741    
6742  checkpoint52m_post  checkpoint52m_post (2004/04/18)
6743  o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;  o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
6744    this does not change any of the results, because myIter=0 in swfrac always    this does not change any of the results, because myIter=0 in swfrac always
6745    lead to jwtype=2 (the default anyway), but the call makes little sense    lead to jwtype=2 (the default anyway), but the call makes little sense
# Line 123  o test exp. advect_cs: use the standard Line 6771  o test exp. advect_cs: use the standard
6771  o Added functionality to grdchk:  o Added functionality to grdchk:
6772    pick global i,j,k position (or nearest wet) where to perform check.    pick global i,j,k position (or nearest wet) where to perform check.
6773    
6774  checkpoint52l_post  checkpoint52l_post (2004/03/11)
6775  o new land formulation:  o new land formulation:
6776    a) use ground enthalpy as prognostic variable to ensure exact    a) use ground enthalpy as prognostic variable to ensure exact
6777       energy conservation.       energy conservation.
# Line 134  o aim_v23 modification for new land mode Line 6782  o aim_v23 modification for new land mode
6782    a) Treat separately land / ocean / sea-ice surface fluxes    a) Treat separately land / ocean / sea-ice surface fluxes
6783       to allow implicit computation of land & sea-ice surface temp.       to allow implicit computation of land & sea-ice surface temp.
6784    b) add snow precipitation.    b) add snow precipitation.
6785  checkpoint52l_pre  checkpoint52l_pre (2004/03/11)
6786    
6787  o fix problem (when 1 tile is empty) in min/max monitor.  o fix problem (when 1 tile is empty) in min/max monitor.
6788  o fix bug in timeAve (u,vZetatave in common block)  o fix bug in timeAve (u,vZetatave in common block)
# Line 147  o fix ini_curvilinear_grid ; test CS exp Line 6795  o fix ini_curvilinear_grid ; test CS exp
6795  o aim.5l_cs: modify sea-ice fraction input file ; update output  o aim.5l_cs: modify sea-ice fraction input file ; update output
6796  o exf: Adding simple range check routine for exf fields after read  o exf: Adding simple range check routine for exf fields after read
6797    
6798  checkpoint52k_post  checkpoint52k_post (2004/02/23)
6799  o removed top-level directory "diags"  o removed top-level directory "diags"
6800    - we migrated these functions to pkg/timeave a long time ago    - we migrated these functions to pkg/timeave a long time ago
6801  o fixed bug introduced in pkg/monitor  o fixed bug introduced in pkg/monitor
# Line 160  o set all ...Freq to zero after cost_fin Line 6808  o set all ...Freq to zero after cost_fin
6808    taveFreq, dumpFreq, pChkptFreq    taveFreq, dumpFreq, pChkptFreq
6809  o MAIN and ECCO differentiability restored  o MAIN and ECCO differentiability restored
6810    
6811  checkpoint52j_post  checkpoint52j_post (2004/02/18)
6812  o fix nchklev in tamc.h for global_ocean...  o fix nchklev in tamc.h for global_ocean...
6813  o Bringing flow and store directives up-to-date  o Bringing flow and store directives up-to-date
6814  o Really weird thing!  o Really weird thing!
# Line 168  o Really weird thing! Line 6816  o Really weird thing!
6816    starttime, niter0, instead of mytime, myiter, screws up the adjoint:    starttime, niter0, instead of mytime, myiter, screws up the adjoint:
6817    TAF places a faulty re-call of initialise_varia    TAF places a faulty re-call of initialise_varia
6818    after cost_final call which should not be there!    after cost_final call which should not be there!
6819  checkpoint52j_pre  checkpoint52j_pre (2004/02/03)
6820    
6821  o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and  o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
6822    error messages    error messages
# Line 185  o merged mom_vi_calc_relvort3.F, mom_vi_ Line 6833  o merged mom_vi_calc_relvort3.F, mom_vi_
6833    mon_vort3.F to make exch2 friendly with >1 tile per cube face    mon_vort3.F to make exch2 friendly with >1 tile per cube face
6834  o limit timeave output for hi-res integrations  o limit timeave output for hi-res integrations
6835    
6836  checkpoint52i_post  checkpoint52i_post (2004/01/21)
6837  o removed CPP_EEOPTIONS.h from verification/*/code  o removed CPP_EEOPTIONS.h from verification/*/code
6838  o updated the tiling for global_ocean_pressure  o updated the tiling for global_ocean_pressure
6839  checkpoint52i_pre  checkpoint52i_pre (2004/01/20)
6840    
6841  o update aim.5l_LatLon using the standard aim_v23 pkg (instead of  o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
6842    the old pkg/aim).    the old pkg/aim).
6843    
6844  checkpoint52h_pre  checkpoint52h_pre (2004/01/20)
6845  o shortened offending lines in exch2_send_rx?.template  o shortened offending lines in exch2_send_rx?.template
6846  o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator  o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
6847  o genmake2: add build & execute test for NetCDF code  o genmake2: add build & execute test for NetCDF code
# Line 204  o added temporary hack for sea-ice dynam Line 6852  o added temporary hack for sea-ice dynam
6852    metric terms are ignored and it is assumed that    metric terms are ignored and it is assumed that
6853    there is no sea-ice on cube faces 1, 2, 4, and 5.    there is no sea-ice on cube faces 1, 2, 4, and 5.
6854    
6855  checkpoint52f_post  checkpoint52f_post (2004/01/09)
6856  o added exch2 cube routines to pkg/exch2  o added exch2 cube routines to pkg/exch2
6857  o modified hs94.cs-32x32x5 to use it  o modified hs94.cs-32x32x5 to use it
6858  o added new grid files to hs94.cs-32x32x5  o added new grid files to hs94.cs-32x32x5
6859  checkpoint52f_pre  checkpoint52f_pre (2004/01/07)
6860    
6861  checkpoint52e_post  checkpoint52e_post (2004/01/07)
6862  o first attempt to solve vertical advection (momemtum & T,S) Implicitly  o first attempt to solve vertical advection (momemtum & T,S) Implicitly
6863    for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)    for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
6864  o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)  o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
# Line 218  o step.1 : rewrite (as in MultiDimAdvec) Line 6866  o step.1 : rewrite (as in MultiDimAdvec)
6866  o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.  o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
6867  o update output (gad_calc_rhs.F changes affect truncation error) of exp:  o update output (gad_calc_rhs.F changes affect truncation error) of exp:
6868   front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box   front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
6869  checkpoint52e_pre  checkpoint52e_pre (2004/01/02)
6870    
6871  o fix bug in impldiff when Nr=1 or Nr=2.  o fix bug in impldiff when Nr=1 or Nr=2.
6872  o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt  o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
# Line 229  o added exf_offset_atemp for Celsius to Line 6877  o added exf_offset_atemp for Celsius to
6877  o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024  o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
6878  o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations  o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
6879    
6880  checkpoint52d_post  checkpoint52d_post (2003/12/16)
6881  o re-tiled many expts to allow comparison in multi-processor mode  o re-tiled many expts to allow comparison in multi-processor mode
6882    - updated output accordingly    - updated output accordingly
6883    - changed hs94.128x64x5 to use intial T from file rather than use the    - changed hs94.128x64x5 to use intial T from file rather than use the
# Line 258  o check-in the first version of the coup Line 6906  o check-in the first version of the coup
6906  o new verification experiment, cpl_aim+ocn:  o new verification experiment, cpl_aim+ocn:
6907     coupled ocean - AIM atmosphere on cs32 grid.     coupled ocean - AIM atmosphere on cs32 grid.
6908    
6909  checkpoint52d_pre  checkpoint52d_pre (2003/12/06)
6910  o surface flux time-av diagnostic modified for NLFS & RealFreshWater  o surface flux time-av diagnostic modified for NLFS & RealFreshWater
6911  o add call to AIM pendant S/R in external_forcing & external_fields_load.F  o add call to AIM pendant S/R in external_forcing & external_fields_load.F
6912    
6913  checkpoint52c_post  checkpoint52c_post (2003/11/25)
6914  o Fixing OPTIONS files for use of exf:  o Fixing OPTIONS files for use of exf:
6915    - ALLOW_ECCO not needed    - ALLOW_ECCO not needed
6916    - ECCO_CPPOPTIONS.h should not be included from    - ECCO_CPPOPTIONS.h should not be included from
# Line 276  o Removed all CPP options for cal packag Line 6924  o Removed all CPP options for cal packag
6924  o modified STOREs in GAD_ADVECTION  o modified STOREs in GAD_ADVECTION
6925  o corrected key comp. for passkey  o corrected key comp. for passkey
6926    
6927  checkpoint52b_post  checkpoint52b_post (2003/11/23)
6928  o new version: "thsice" of thermodynamic sea-ice pkg:  o new version: "thsice" of thermodynamic sea-ice pkg:
6929   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
6930   - modify fluxes but do not change theta directly;   - modify fluxes but do not change theta directly;
# Line 284  o new version: "thsice" of thermodynamic Line 6932  o new version: "thsice" of thermodynamic
6932   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
6933     + output_thsice.txt to test thsice & bulk_force pkgs.     + output_thsice.txt to test thsice & bulk_force pkgs.
6934  o put back grid & coriolis monitor output.  o put back grid & coriolis monitor output.
6935  checkpoint52b_pre  checkpoint52b_pre (2003/11/23)
6936    
6937  o call "do_the_model_io" at the beginning (=> dump initial state)  o call "do_the_model_io" at the beginning (=> dump initial state)
6938  o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)  o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
# Line 294  o missing PTRACERS headers in some routi Line 6942  o missing PTRACERS headers in some routi
6942  o default tamc.h in pkg/autodiff supposed to crash  o default tamc.h in pkg/autodiff supposed to crash
6943    to ensure proper customization    to ensure proper customization
6944    
6945  checkpoint52a_post  checkpoint52a_post (2003/11/17)
6946  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
6947    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
6948    - subroutine FREEZE_SURFACE now limits only surface temperature    - subroutine FREEZE_SURFACE now limits only surface temperature
# Line 309  o fix problem with ECCO-related divided Line 6957  o fix problem with ECCO-related divided
6957    snapshot file was missing some ad-variables,    snapshot file was missing some ad-variables,
6958    but no warning issued by TAF    but no warning issued by TAF
6959    
6960  checkpoint52a_pre  checkpoint52a_pre (2003/11/12)
6961  o some bug fixes for #undef REAL4_IS_SLOW  o some bug fixes for #undef REAL4_IS_SLOW
6962    
6963  checkpoint52 = ecco_c52_e35  checkpoint52 = ecco_c52_e35
6964  o after testing adjoints of checkpoint51u_post  o after testing adjoints of checkpoint51u_post
6965    
6966  checkpoint51u_post  checkpoint51u_post (2003/11/06)
6967  o this is the post-merge tag of the ecco-branch  o this is the post-merge tag of the ecco-branch
6968    (needs another clean checkout and re-testing)    (needs another clean checkout and re-testing)
6969  o various natl_box_adjoint configs and results  o various natl_box_adjoint configs and results
# Line 330  o top level routines the_main_loop, forw Line 6978  o top level routines the_main_loop, forw
6978    (new namelist ecco_cost_nml)    (new namelist ecco_cost_nml)
6979  o in ctrl/ cleaned some cross-dependencies and updated CPP options  o in ctrl/ cleaned some cross-dependencies and updated CPP options
6980    
6981  checkpoint51t_post  checkpoint51t_post (2003/11/04)
6982  o this is the pre-merge tag of the ecco-branch  o this is the pre-merge tag of the ecco-branch
6983    
6984  checkpoint51s_post  checkpoint51s_post (2003/11/04)
6985  o cleanup: removed various obsolete #define-s  o cleanup: removed various obsolete #define-s
6986  o pkg/grdchk  o pkg/grdchk
6987    - renamed 'ph-grd 3' to 'grad-res'    - renamed 'ph-grd 3' to 'grad-res'
# Line 342  o pkg/grdchk Line 6990  o pkg/grdchk
6990    - additional high-precision output for testreport    - additional high-precision output for testreport
6991      (grep for 'precision_grdchk_result')      (grep for 'precision_grdchk_result')
6992    
6993  checkpoint51r_post  checkpoint51r_post (2003/11/03)
6994  o cleaned up or removed CPP_OPTIONS.h files  o cleaned up or removed CPP_OPTIONS.h files
6995  o updated results for some of the tests to reflect the new  o updated results for some of the tests to reflect the new
6996    optfiles (-ieee: -O0 instead of -O3)    optfiles (-ieee: -O0 instead of -O3)
6997    
6998  checkpoint51q_post  checkpoint51q_post (2003/10/30)
6999  o cd_code:  o cd_code:
7000    - moved cd_scheme.F -> cd_code_scheme.F    - moved cd_scheme.F -> cd_code_scheme.F
7001    - separate read_checkpoint from cd_code_ini_vars.F    - separate read_checkpoint from cd_code_ini_vars.F
# Line 363  o ctrl package totally restructured Line 7011  o ctrl package totally restructured
7011    - confined inclusion of AD_CONFIG.h to where necessary.    - confined inclusion of AD_CONFIG.h to where necessary.
7012  o genmake2: changed AD dependencies from SRCFILES to AD_FILES  o genmake2: changed AD dependencies from SRCFILES to AD_FILES
7013    
7014  checkpoint51p_post  checkpoint51p_post (2003/10/30)
7015  o create initial cd_code package  o create initial cd_code package
7016    - WARNING: the initialization of fields within packages    - WARNING: the initialization of fields within packages
7017      is broken because INI_FIELDS (where READ_CHECKPOINT is      is broken because INI_FIELDS (where READ_CHECKPOINT is
# Line 378  o create initial cd_code package Line 7026  o create initial cd_code package
7026  o cleanup verification/*/code/GMREDI_OPTIONS.h  o cleanup verification/*/code/GMREDI_OPTIONS.h
7027  o cleanup testreport  o cleanup testreport
7028    
7029  checkpoint51o_post  checkpoint51o_post (2003/10/27)
7030  o bringing AD-related verif's up to date with genmake2  o bringing AD-related verif's up to date with genmake2
7031    - carbon/    - carbon/
7032    - global_ocean.90x40x15/    - global_ocean.90x40x15/
# Line 399  o Correcting initialisations for fVerU, Line 7047  o Correcting initialisations for fVerU,
7047  o helping TAF to recognize dependency on kUp for  o helping TAF to recognize dependency on kUp for
7048    fVerU, fVerV    fVerU, fVerV
7049  o Replacing delZ by delR in pkg/ctrl/  o Replacing delZ by delR in pkg/ctrl/
7050  checkpoint51o_pre  checkpoint51o_pre (2003/10/24)
7051    
7052  o undid all of cp51 pending some cleanups and discussion  o undid all of cp51 pending some cleanups and discussion
7053  o added the [#include "AD_CONFIG.h"] statement to all files that need  o added the [#include "AD_CONFIG.h"] statement to all files that need
# Line 407  o added the [#include "AD_CONFIG.h"] sta Line 7055  o added the [#include "AD_CONFIG.h"] sta
7055   o re-worked the build logic in genmake2 to support AD_CONFIG.h   o re-worked the build logic in genmake2 to support AD_CONFIG.h
7056   o removed tools/genmake since it no longer works   o removed tools/genmake since it no longer works
7057    
7058  checkpoint51n_post  checkpoint51n_post (2003/10/23)
7059  o modifications to make FREEZE flux visible to pkg/kpp  o modifications to make FREEZE flux visible to pkg/kpp
7060    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
7061    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
# Line 416  o modifications to make FREEZE flux visi Line 7064  o modifications to make FREEZE flux visi
7064       global_ocean.cs32x15, and global_with_exf)       global_ocean.cs32x15, and global_with_exf)
7065  o added surface flux output variables to TIMEAVE_STATVARS  o added surface flux output variables to TIMEAVE_STATVARS
7066    
7067  checkpoint51n_pre  checkpoint51n_pre (2003/10/23)
7068  o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F  o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
7069  o added [#include "AD_CONFIG.h"] to all files that use the following  o added [#include "AD_CONFIG.h"] to all files that use the following
7070    defines:    defines:
# Line 424  o added [#include "AD_CONFIG.h"] to all Line 7072  o added [#include "AD_CONFIG.h"] to all
7072    - ALLOW_TANGENTLINEAR_RUN    - ALLOW_TANGENTLINEAR_RUN
7073    - ALLOW_ECCO_OPTIMIZATION    - ALLOW_ECCO_OPTIMIZATION
7074    
7075  checkpoint51m_post  checkpoint51m_post (2003/10/21)
7076  o incorporating changes to get TAMC/TAF working in genmake2  o incorporating changes to get TAMC/TAF working in genmake2
7077    - added new TAMC/TAF targets to the Makefile    - added new TAMC/TAF targets to the Makefile
7078    - various cleanups related to package handling    - various cleanups related to package handling
7079    - these changes should have no impact on the forward model    - these changes should have no impact on the forward model
7080    
7081  checkpoint51l_post  checkpoint51l_post (2003/10/20)
7082  o changes to pkg/cal and pkg/exf that allow and speed-up long integrations  o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
7083   - faster algorithm for cal_addtime.F   - faster algorithm for cal_addtime.F
7084   - higher precision arithmetic, where needed   - higher precision arithmetic, where needed
7085   - pkg/exf *startdate variables changed from calendar date to   - pkg/exf *startdate variables changed from calendar date to
7086     model integration time     model integration time
7087    
7088  checkpoint51l_pre  checkpoint51l_pre (2003/10/17)
7089  o add salt flux to forcing fields (used when salty sea-ice forms or melts)  o add salt flux to forcing fields (used when salty sea-ice forms or melts)
7090  o enable to apply restoring on S & T only in a latitude band.  o enable to apply restoring on S & T only in a latitude band.
7091  o update output (external_forcing_surf modif. change truncation errors)  o update output (external_forcing_surf modif. change truncation errors)
7092     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
7093    
7094  checkpoint51k_post  checkpoint51k_post (2003/10/16)
7095  o change default to: useNHMTerms=.FALSE.  o change default to: useNHMTerms=.FALSE.
7096   - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):   - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
7097     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
# Line 457  o added an include barrier to the defaul Line 7105  o added an include barrier to the defaul
7105    removed the #include "PACKAGES_CONFIG.h" from it    removed the #include "PACKAGES_CONFIG.h" from it
7106  o fix a bug in mom_fluxform (from chk51j_post)  o fix a bug in mom_fluxform (from chk51j_post)
7107    
7108  checkpoint51j_post  checkpoint51j_post (2003/10/10)
7109  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
7110  o adjusted some flow directives (dynamics, thermodynamics)  o adjusted some flow directives (dynamics, thermodynamics)
7111  o added cubed-sphere case to test cost function  o added cubed-sphere case to test cost function
# Line 471  o Moving pkg-specific flow directives to Line 7119  o Moving pkg-specific flow directives to
7119         - pkg_ad_diff.list         - pkg_ad_diff.list
7120         - pkg_ad_check_lev?_dir.h         - pkg_ad_check_lev?_dir.h
7121    
7122  checkpoint51i_post  checkpoint51i_post (2003/10/09)
7123  o merge of the branch-genmake2  o merge of the branch-genmake2
7124    - knowingly breaks the older genmake    - knowingly breaks the older genmake
7125    - automatic generation of all ALLOW_${PKG_NAME} defines    - automatic generation of all ALLOW_${PKG_NAME} defines
7126    - new testreport supersedes older testscript    - new testreport supersedes older testscript
7127  o large number of package inclusion and header cleanups  o large number of package inclusion and header cleanups
7128  checkpoint51i_pre  checkpoint51i_pre (2003/10/08)
7129    
7130  o new output for adjoin of global ocean vector invariant  o new output for adjoin of global ocean vector invariant
7131  o fix for checkpoint of thermodynamic seaice and bulk_force  o fix for checkpoint of thermodynamic seaice and bulk_force
# Line 489  o modify gchem pkg to be more versatile Line 7137  o modify gchem pkg to be more versatile
7137  o modifications to clean up dic pkg  o modifications to clean up dic pkg
7138  o add pkg/cfc  o add pkg/cfc
7139    
7140  checkpoint51g_post  checkpoint51g_post (2003/10/02)
7141  o provide links for ARPACK and ADM*TLM  o provide links for ARPACK and ADM*TLM
7142  o start removing verification/vero/  o start removing verification/vero/
7143  o update AD-related stuff  o update AD-related stuff
# Line 497  o update AD-related stuff Line 7145  o update AD-related stuff
7145  o adding to verification/global_ocean.90x40x15/ adjoint of  o adding to verification/global_ocean.90x40x15/ adjoint of
7146    vector invariant setup    vector invariant setup
7147    
7148  checkpoint51f_post  checkpoint51f_post (2003/10/02)
7149  o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)  o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
7150  o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation  o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
7151    of tracer Green's fucntions for ocean inversion project.    of tracer Green's fucntions for ocean inversion project.
7152    
7153  checkpoint51f_pre  checkpoint51f_pre (2003/08/07)
7154  o Added on-the-fly spatial interpolation capability  o Added on-the-fly spatial interpolation capability
7155      "USE_EXF_INTERPOLATION" to pkg/exf.      "USE_EXF_INTERPOLATION" to pkg/exf.
7156    - This is a temporary Cartesian-grid hack until    - This is a temporary Cartesian-grid hack until
# Line 514  o Bug fix to pkg/ptracers, pkg/generic_a Line 7162  o Bug fix to pkg/ptracers, pkg/generic_a
7162      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
7163      non-local transport term.      non-local transport term.
7164    
7165  checkpoint51e_post  checkpoint51e_post (2003/08/03)
7166  o pkg/mom_vecinv:  o pkg/mom_vecinv:
7167    - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)    - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
7168    - add time-ave diagnostic of vorticity advection.    - add time-ave diagnostic of vorticity advection.
# Line 524  o atmospheric geopotential: - include wa Line 7172  o atmospheric geopotential: - include wa
7172  o land pkg: read initial state from files.  o land pkg: read initial state from files.
7173  o AIM : add stratospheric drag in the upper level  o AIM : add stratospheric drag in the upper level
7174    
7175  checkpoint51d_post  checkpoint51d_post (2003/07/18)
7176  o change function ILNBLNK (=> last non-blank char.) to return zero  o change function ILNBLNK (=> last non-blank char.) to return zero
7177    (instead of the string length) when the string. char is empty    (instead of the string length) when the string. char is empty
7178  o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)  o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
# Line 537  o Use cluster local disks for purely loc Line 7185  o Use cluster local disks for purely loc
7185    - new active_file_loc... and mdsio_..._loc routines    - new active_file_loc... and mdsio_..._loc routines
7186    - affected packages: autodiff, ctrl, grdchk, mdsio    - affected packages: autodiff, ctrl, grdchk, mdsio
7187    
7188  checkpoint51c_post  checkpoint51c_post (2003/07/08)
7189  o introducing integer flag debugLevel  o introducing integer flag debugLevel
7190    - debLevZero: suppress all output    - debLevZero: suppress all output
7191    - debLevA: standard    - debLevA: standard
# Line 560  o added verification for adjoint with pt Line 7208  o added verification for adjoint with pt
7208    - checked tapelev/comlev recomputations: OK    - checked tapelev/comlev recomputations: OK
7209  <<<checkpoint51b_pre  <<<checkpoint51b_pre
7210    
7211  checkpoint51a_post  checkpoint51a_post (2003/06/25)
7212  o added code for biogeochemistry package  o added code for biogeochemistry package
7213    - new pkgs: dic, gchem    - new pkgs: dic, gchem
7214    - new subroutine in ptracers    - new subroutine in ptracers
7215  o modify code for biogeo packages  o modify code for biogeo packages
7216    - in model/src and pkg/ptracers    - in model/src and pkg/ptracers
7217    
7218  checkpoint51  checkpoint51 (2003/06/24)
7219  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
7220    - autodiff, ctrl, exf, grdchk, seaice    - autodiff, ctrl, exf, grdchk, seaice
7221    kept separate packages    kept separate packages
# Line 575  o merged improved packages from ecco-bra Line 7223  o merged improved packages from ecco-bra
7223  o updating verification/internal_wave, verification/lab_sea  o updating verification/internal_wave, verification/lab_sea
7224    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
7225    
7226  checkpoint50i_post  checkpoint50i_post (2003/06/23)
7227  o Preparing next differentiable checkpoint and sync  o Preparing next differentiable checkpoint and sync
7228    of MAIN vs. ecco-branch    of MAIN vs. ecco-branch
7229    - 1st step: this one is differentiable    - 1st step: this one is differentiable
7230    - 2nd step: next(! not this) checkpoint will have updated packages    - 2nd step: next(! not this) checkpoint will have updated packages
7231                from ecco-branch)                from ecco-branch)
7232    
7233  checkpoint50h_post  checkpoint50h_post (2003/06/20)
7234  o new package "land": provide surface BC for AIM.  o new package "land": provide surface BC for AIM.
7235  o pkg/ptracers: apply exchange to all tracers after reading a pickup.  o pkg/ptracers: apply exchange to all tracers after reading a pickup.
7236  o AIM: use true log-P extrapolation for near surface temp (= as in  o AIM: use true log-P extrapolation for near surface temp (= as in
# Line 591  o New variable in PARM03 for more flexib Line 7239  o New variable in PARM03 for more flexib
7239  o somewhat cleaned package initialisation sequence for  o somewhat cleaned package initialisation sequence for
7240    ctrl/ cost/ ecco/ in packages_... routines    ctrl/ cost/ ecco/ in packages_... routines
7241    
7242  checkpoint50g_post  checkpoint50g_post (2003/05/23)
7243  o merged with release1_p17 (pkg/seaice and verification/lab_sea)  o merged with release1_p17 (pkg/seaice and verification/lab_sea)
7244    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
7245    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
7246      made the default because of faster convergence than ADI      made the default because of faster convergence than ADI
7247    
7248  checkpoint50f_post  checkpoint50f_post (2003/05/23)
7249  o exf totally restructured  o exf totally restructured
7250    - replaced all exf_set_ routines by one generic exf_set_gen.F    - replaced all exf_set_ routines by one generic exf_set_gen.F
7251      and made sure it's still differentiable      and made sure it's still differentiable
# Line 605  o exf totally restructured Line 7253  o exf totally restructured
7253    - exf_inscal_/exf_outscal_ suffixes consistent with field names    - exf_inscal_/exf_outscal_ suffixes consistent with field names
7254    - updated adjoint/makefile and relevant verif. accordingly    - updated adjoint/makefile and relevant verif. accordingly
7255    
7256  checkpoint50f_pre  checkpoint50f_pre (2003/05/23)
7257   o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;   o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
7258        + change Evap over land. (update aim.5l_cs output)        + change Evap over land. (update aim.5l_cs output)
7259   o added missing .cvsignores and made uniform across expts   o added missing .cvsignores and made uniform across expts
# Line 615  checkpoint50f_pre Line 7263  checkpoint50f_pre
7263   o new fn in pkg/monitor to stop model if solution grows too big   o new fn in pkg/monitor to stop model if solution grows too big
7264   o removed lots of single quotes from comments   o removed lots of single quotes from comments
7265    
7266  checkpoint50e_post  checkpoint50e_post (2003/05/14)
7267  o make KPP work with PTRACERS  o make KPP work with PTRACERS
7268   - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is   - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
7269     nearly a copy of kpp_transport_s     nearly a copy of kpp_transport_s
7270   - there is no analogue to SurfaceTendencyS, so I have to use   - there is no analogue to SurfaceTendencyS, so I have to use
7271     gPtr(of the surface layer) instead     gPtr(of the surface layer) instead
7272  o add a new platform SunFire+mpi (SunFire 15000) to genmake  o add a new platform SunFire+mpi (SunFire 15000) to genmake
7273  checkpoint50e_pre  checkpoint50e_pre (2003/05/13)
7274    
7275  checkpoint50d_post  checkpoint50d_post (2003/05/13)
7276  o change kpp output from multiple-record state files to single-record state  o change kpp output from multiple-record state files to single-record state
7277    files analogous to write_state.F    files analogous to write_state.F
7278  o reduce the output frequency of cg3d-related stuff to the monitor frequency,  o reduce the output frequency of cg3d-related stuff to the monitor frequency,
7279    analogous to the cg2d-related output.    analogous to the cg2d-related output.
7280  o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,  o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
7281    so that writing to internal file fn (with length 512) fails.    so that writing to internal file fn (with length 512) fails.
7282  checkpoint50d_pre  checkpoint50d_pre (2003/05/12)
7283    
7284  checkpoint50c_post  checkpoint50c_post (2003/05/12)
7285  o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)  o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
7286  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
7287  o add time-average diagnostic of U*V and vertical diffusive flux for theta.  o add time-average diagnostic of U*V and vertical diffusive flux for theta.
7288  o bug fixed in convective adjustment diagnostic (multi-tile set-up).  o bug fixed in convective adjustment diagnostic (multi-tile set-up).
7289  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
7290    
7291  checkpoint50c_pre  checkpoint50c_pre (2003/04/30)
7292  Merging from release1_p13:  Merging from release1_p13:
7293  o bug fix for pkg/seaice dynamic solver  o bug fix for pkg/seaice dynamic solver
7294  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
7295    
7296  checkpoint50b_post  checkpoint50b_post (2003/04/17)
7297  o store u*,v* in gU,V instead of in guNm1,gvNm1  o store u*,v* in gU,V instead of in guNm1,gvNm1
7298  o in order to put the momForcing out of the Adams-Bashforth:  o in order to put the momForcing out of the Adams-Bashforth:
7299    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
# Line 654  o new flag "useCDscheme" (default=F); re Line 7302  o new flag "useCDscheme" (default=F); re
7302  o re-generate output for highly sensitive test-exp:  o re-generate output for highly sensitive test-exp:
7303     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
7304    
7305  checkpoint50b_pre  checkpoint50b_pre (2003/04/17)
7306  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
7307  o corrected CPP option mismatch in exf_Bulk... functions for case  o corrected CPP option mismatch in exf_Bulk... functions for case
7308    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
7309    
7310  checkpoint50a_post  checkpoint50a_post (2003/03/21)
7311  o Bug fix for merging between c50 and KPP.  o Bug fix for merging between c50 and KPP.
7312    ikey was passed from thermodynamics to kpp_calc via    ikey was passed from thermodynamics to kpp_calc via
7313    common block rather than being recomputed in kpp_calc,    common block rather than being recomputed in kpp_calc,
7314    in contradiction with new key itdkey.    in contradiction with new key itdkey.
7315    New key ikppkey created, and tamc.h headers updated.    New key ikppkey created, and tamc.h headers updated.
7316    
7317  checkpoint50  checkpoint50 (2003/03/08)
7318  - 2nd step of merge with ecco-branch:  - 2nd step of merge with ecco-branch:
7319    merge changes in ecco-branch back into main trunk    merge changes in ecco-branch back into main trunk
7320  - bug fix in find_alpha  - bug fix in find_alpha
# Line 674  checkpoint50 Line 7322  checkpoint50
7322  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
7323  - merged some sliced AD support routines  - merged some sliced AD support routines
7324    
7325  checkpoint49  checkpoint49 (2003/03/06)
7326  merged from ecco-branch:  merged from ecco-branch:
7327  o exf:  o exf:
7328    - Enable initialisation of forcing fields to constant    - Enable initialisation of forcing fields to constant
# Line 712  o DIVA: Line 7360  o DIVA:
7360    (see MITgcm manual).    (see MITgcm manual).
7361  o cal: synchronized between MAIN and ecco-branch  o cal: synchronized between MAIN and ecco-branch
7362    
7363  checkpoint48i_post  checkpoint48i_post (2003/03/05)
7364  o Changes to restore differentiability of code w.r.t. previous tag  o Changes to restore differentiability of code w.r.t. previous tag
7365    (mostly adding new routines to make list and replacing    (mostly adding new routines to make list and replacing
7366    pressure by totPhiHyd).    pressure by totPhiHyd).
# Line 730  o Modif. for DIVA: Line 7378  o Modif. for DIVA:
7378    tbar, sbar, psbar, which should not be reinitialised;    tbar, sbar, psbar, which should not be reinitialised;
7379    only relevant for ecco-branch)    only relevant for ecco-branch)
7380    
7381  checkpoint48h_post  checkpoint48h_post (2003/02/28)
7382  o improve "ini_p_ground" when using finite difference form for calc_phi_hyd  o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
7383  o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F  o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
7384  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
7385  o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT  o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
7386    
7387  checkpoint48g_post  checkpoint48g_post (2003/02/18)
7388  --- EOS:  --- EOS:
7389  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
7390    store total Potential in totPhyHyd for diagnostics & EOS.    store total Potential in totPhyHyd for diagnostics & EOS.
# Line 750  o accurate phiHyd when using interface-W Line 7398  o accurate phiHyd when using interface-W
7398   ( changes results of ideal_2D_oce )   ( changes results of ideal_2D_oce )
7399  o includes r* 2nd term in potential gradient.  o includes r* 2nd term in potential gradient.
7400    
7401  checkpoint48f_post  checkpoint48f_post (2003/02/18)
7402  Merging from release1_p12:  Merging from release1_p12:
7403  o Modifications for using pkg/exf with pkg/seaice  o Modifications for using pkg/exf with pkg/seaice
7404    - improved description of the various forcing configurations    - improved description of the various forcing configurations
# Line 778  o pkg/seaice: Line 7426  o pkg/seaice:
7426    - adjoint-friendly modifications    - adjoint-friendly modifications
7427    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
7428    
7429  checkpoint48e_post  checkpoint48e_post (2003/02/12)
7430  o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)  o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
7431  o dynamics: change definition of computational domain & adapt mom_fluxform  o dynamics: change definition of computational domain & adapt mom_fluxform
7432    accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.    accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
# Line 789  o following exp works with Olx=Oly=2 (an Line 7437  o following exp works with Olx=Oly=2 (an
7437      inverted_barometer solid-body.cs-32x32x1      inverted_barometer solid-body.cs-32x32x1
7438    (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)    (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
7439    
7440  checkpoint48d_post  checkpoint48d_post (2003/02/09)
7441  o in preparation for r*:  o in preparation for r*:
7442   a) use pre-computed gradient of hydrostatic potential:   a) use pre-computed gradient of hydrostatic potential:
7443      changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce      changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
# Line 797  o in preparation for r*: Line 7445  o in preparation for r*:
7445      => affects results of glob_oce_pressure (different truncation error)        => affects results of glob_oce_pressure (different truncation error)  
7446    update output.txt of ideal_2D_oce & global_ocean_pressure    update output.txt of ideal_2D_oce & global_ocean_pressure
7447    
7448  checkpoint48d_pre  checkpoint48d_pre (2003/02/08)
7449  o in preparation for r*:  o in preparation for r*:
7450    new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.    new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
7451    pass the 2 comp. of the grad. as arguments to momentum S/R.    pass the 2 comp. of the grad. as arguments to momentum S/R.
7452    but for the moment, only used if it does not change the results.    but for the moment, only used if it does not change the results.
7453  o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP  o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
7454    
7455  checkpoint48c_post  checkpoint48c_post (2003/02/06)
7456  Modifications in treatment of initial flux forcing controls  Modifications in treatment of initial flux forcing controls
7457  to avoid extra storing of flux fields.  to avoid extra storing of flux fields.
7458    
7459  checkpoint48c_pre  checkpoint48c_pre (2003/01/21)
7460  o Added tidal_basin_2d experiment (currently 1D!)  o Added tidal_basin_2d experiment (currently 1D!)
7461  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)
7462    
7463  checkpoint48b_post  checkpoint48b_post (2003/01/27)
7464  o r* coordinate added in #ifdef NONLIN_FRSURF block.  o r* coordinate added in #ifdef NONLIN_FRSURF block.
7465   (modification to pressure gradient not yet implemented)   (modification to pressure gradient not yet implemented)
7466  o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports  o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
7467    (for U & V) that are used for vertical advection of momentum.    (for U & V) that are used for vertical advection of momentum.
7468    
7469  checkpoint48a_post  checkpoint48a_post (2003/01/24)
7470  o In preparation for r*, use temp. array to compute vertical transport  o In preparation for r*, use temp. array to compute vertical transport
7471     in flux-form momentum pkg. => change results of few test-exp.     in flux-form momentum pkg. => change results of few test-exp.
7472    Update output of: exp4, exp5, front_relax, global_ocean_pressure,    Update output of: exp4, exp5, front_relax, global_ocean_pressure,
7473                      lab_sea, natl_box & plume_on_slope                      lab_sea, natl_box & plume_on_slope
7474    
7475  checkpoint48  checkpoint48 (2003/01/23)
7476  o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')  o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
7477    
7478  checkpoint47j_post  checkpoint47j_post (2003/01/21)
7479  o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.  o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
7480  o moved adexch from forward_step to addummy_in_stepping  o moved adexch from forward_step to addummy_in_stepping
7481  o added exch in ctrl_map_...  o added exch in ctrl_map_...
# Line 846  o Yet more changes in gmredi: Line 7494  o Yet more changes in gmredi:
7494      re-activated full calculation of taperfct for case 'ac02'      re-activated full calculation of taperfct for case 'ac02'
7495  o updating verification/ adjoints of carbon, global_ocean.90x40x15  o updating verification/ adjoints of carbon, global_ocean.90x40x15
7496    
7497  checkpoint47i_post  checkpoint47i_post (2003/01/13)
7498  o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.  o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
7499  o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)  o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
7500    default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)    default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
# Line 862  o case GM_BOLUS_ADVEC should be cleaned Line 7510  o case GM_BOLUS_ADVEC should be cleaned
7510    S/R gmredi_slope_psi should be cleaned    S/R gmredi_slope_psi should be cleaned
7511  o verification/carbon now has exactConserv=.TRUE.  o verification/carbon now has exactConserv=.TRUE.
7512    
7513  checkpoint47g_post  checkpoint47g_post (2003/01/10)
7514  o time-average AIM output: becomes independent from statvars time-average  o time-average AIM output: becomes independent from statvars time-average
7515    (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)    (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
7516  o After TAF bug fix:  o After TAF bug fix:
# Line 888  Gradient checks OK for Line 7536  Gradient checks OK for
7536  in conjunction with data.gmredi parameters to be checked in  in conjunction with data.gmredi parameters to be checked in
7537  in a few minutes under verification/carbon/code/  in a few minutes under verification/carbon/code/
7538    
7539  checkpoint47f_post  checkpoint47f_post (2002/12/28)
7540  Merging from release1_p10:  Merging from release1_p10:
7541  o modifications for using pkg/exf with pkg/seaice  o modifications for using pkg/exf with pkg/seaice
7542    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
# Line 900  o modifications for using pkg/exf with p Line 7548  o modifications for using pkg/exf with p
7548    - verification/lab_sea default experiment now uses    - verification/lab_sea default experiment now uses
7549      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
7550    
7551  checkpoint47e_post  checkpoint47e_post (2002/12/27)
7552  o created a tag prior to creating a branch  o created a tag prior to creating a branch
7553    
7554  checkpoint47d_post  checkpoint47d_post (2002/12/16)
7555  o fixed bug in the oceanic pressure coordinates code: vertical viscosity  o fixed bug in the oceanic pressure coordinates code: vertical viscosity
7556    at the bottom boundary had an erroneous half slip boundary condition    at the bottom boundary had an erroneous half slip boundary condition
7557  o added bottom drag and no slip boundary condition capabilities to  o added bottom drag and no slip boundary condition capabilities to
7558    oceanic pressure coordinates code    oceanic pressure coordinates code
7559  o added new verification experiment global_ocean_pressure, this experiment is  o added new verification experiment global_ocean_pressure, this experiment is
7560    also described in the tutorial section of the manual    also described in the tutorial section of the manual
7561  checkpoint47d_pre  checkpoint47d_pre (2002/12/16)
7562    
7563  checkpoint47c_post  checkpoint47c_post (2002/12/16)
7564  o Added a verification experiment for a global cubed-sphere ocean run  o Added a verification experiment for a global cubed-sphere ocean run
7565    -  verification/global_ocean.cubed32x32x30    -  verification/global_ocean.cubed32x32x30
7566    -  uses pkg/therm_seaice and pkg/bulk_forcing    -  uses pkg/therm_seaice and pkg/bulk_forcing
# Line 924  o OCEANICP & realFreshWater: include P-E Line 7572  o OCEANICP & realFreshWater: include P-E
7572    NOTES: requires option NONLIN_FRSURF to be "#define".    NOTES: requires option NONLIN_FRSURF to be "#define".
7573  o update advect_xz/results/output.txt (left from checkpoint44g_post)  o update advect_xz/results/output.txt (left from checkpoint44g_post)
7574    
7575  checkpoint47b_post  checkpoint47b_post (2002/12/05)
7576  Merging from release1_p9:  Merging from release1_p9:
7577  o pkg/seaice  o pkg/seaice
7578    - removed GOTO's and added taf directives    - removed GOTO's and added taf directives
# Line 941  o verification/lab_sea Line 7589  o verification/lab_sea
7589    - added missing matlab routines    - added missing matlab routines
7590    - added test of thermodynamics parallelization    - added test of thermodynamics parallelization
7591    
7592  checkpoint47a_post  checkpoint47a_post (2002/11/23)
7593  o new pkg: aim_v23  o new pkg: aim_v23
7594   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
7595     for now, keep the same surface forcing as before.     for now, keep the same surface forcing as before.
# Line 958  o bulk_force and therm_seaice Line 7606  o bulk_force and therm_seaice
7606  - Two ifdef statements for compile time,  - Two ifdef statements for compile time,
7607     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
7608    
7609  checkpoint47  checkpoint47 (2002/11/15)
7610  differentiable version of checkpoint46n_post  differentiable version of checkpoint46n_post
7611  o bug fix in quasihydrostaticterms  o bug fix in quasihydrostaticterms
7612  o * "clean" adjoint code (in terms of extensive recomputations)  o * "clean" adjoint code (in terms of extensive recomputations)
# Line 987  o Updated verification/carbon/ Line 7635  o Updated verification/carbon/
7635    - #define GM_VISBECK_VARIABLE_K    - #define GM_VISBECK_VARIABLE_K
7636    - GM_taper_scheme    = 'ldd97'        - GM_taper_scheme    = 'ldd97'    
7637    
7638  checkpoint46n_post  checkpoint46n_post (2002/11/12)
7639  Merging from release1_p8:  Merging from release1_p8:
7640  o verification/natl_box:  o verification/natl_box:
7641    updating new external_fields_load routine    updating new external_fields_load routine
# Line 1041  o Adding new verification experiment glo Line 7689  o Adding new verification experiment glo
7689    the exf (and cal) package instead of the    the exf (and cal) package instead of the
7690    external_fields_load routine (cf README file).    external_fields_load routine (cf README file).
7691    
7692  checkpoint46m_post  checkpoint46m_post (2002/11/07)
7693  o modified testscript to return -- when there are no lines of "%MON" output  o modified testscript to return -- when there are no lines of "%MON" output
7694  o added new flag "quasiHydrostatic" for QH mode  o added new flag "quasiHydrostatic" for QH mode
7695    and new routine quasihydrostaticterms()    and new routine quasihydrostaticterms()
# Line 1054  o introduced flag for controllin non-hyd Line 7702  o introduced flag for controllin non-hyd
7702  o removed gravitySign from PARM04  o removed gravitySign from PARM04
7703  o switched to g77/ifc from pgf77 in aim experiments  o switched to g77/ifc from pgf77 in aim experiments
7704    
7705  checkpoint46l_post  checkpoint46l_post (2002/11/01)
7706  o made convective adjustment work with pressure coordinates:  o made convective adjustment work with pressure coordinates:
7707   - changed the direction of k-loop in convective_adjustment.F for the   - changed the direction of k-loop in convective_adjustment.F for the
7708     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
# Line 1067  o made convective adjustment work with p Line 7715  o made convective adjustment work with p
7715     at the beginning of find_rho, find_alpha, and find_beta, does a     at the beginning of find_rho, find_alpha, and find_beta, does a
7716     check of the entire slice, if CPP-option     check of the entire slice, if CPP-option
7717     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
7718  checkpoint46l_pre  checkpoint46l_pre (2002/10/23)
7719    
7720  checkpoint46k_post  checkpoint46k_post (2002/10/23)
7721  o fixed the verification/global_ocean.90x40x15 experiment:  o fixed the verification/global_ocean.90x40x15 experiment:
7722   - new bathymetry (the world according to A., JMC, and M.)   - new bathymetry (the world according to A., JMC, and M.)
7723   - new initial fields and forcing fields (*.bin files)   - new initial fields and forcing fields (*.bin files)
# Line 1083  o S/R aim_initialise.F replace S/R aim_i Line 7731  o S/R aim_initialise.F replace S/R aim_i
7731   - read AIM physics parameters from a file (data.aimphys)   - read AIM physics parameters from a file (data.aimphys)
7732   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
7733    
7734  checkpoint46j_post  checkpoint46j_post (2002/10/07)
7735  o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH  o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
7736  o move wVel computation at the end of the time step, in S/R integr_continuity  o move wVel computation at the end of the time step, in S/R integr_continuity
7737  o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)  o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
7738  o update timeave pkg for wVel diagnostic.  o update timeave pkg for wVel diagnostic.
7739  checkpoint46j_pre  checkpoint46j_pre (2002/09/27)
7740    
7741  checkpoint46i_post  checkpoint46i_post (2002/09/25)
7742  o Clean up AIM package (and keep the results unchanged):  o Clean up AIM package (and keep the results unchanged):
7743    include CPP_OPTION and use IMPLICT NONE in all routines ;    include CPP_OPTION and use IMPLICT NONE in all routines ;
7744    declare all the variables _RL ; use _d 0 for all numerical constants.    declare all the variables _RL ; use _d 0 for all numerical constants.
7745    use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !    use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
7746    
7747  checkpoint46h_post  checkpoint46h_post (2002/09/25)
7748  o cleaned up the use of rhoNil and rhoConst.  o cleaned up the use of rhoNil and rhoConst.
7749    - rhoNil should only appear in the LINEAR equation of state, everywhere    - rhoNil should only appear in the LINEAR equation of state, everywhere
7750      else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst      else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
# Line 1106  o introduced new parameter rhoConstFresh Line 7754  o introduced new parameter rhoConstFresh
7754    value is 999.8 kg/m^3    value is 999.8 kg/m^3
7755  o cleanup up external_forcing.F and external_forcing_surf.F  o cleanup up external_forcing.F and external_forcing_surf.F
7756    - can now be used by both OCEANIC and OCEANICP    - can now be used by both OCEANIC and OCEANICP
7757  checkpoint46h_pre  checkpoint46h_pre (2002/09/18)
7758    
7759   Added code to convert surface volume flux (fresh water) into   Added code to convert surface volume flux (fresh water) into
7760   a mass flux when using P coordinates in the ocean (OCEANICP).   a mass flux when using P coordinates in the ocean (OCEANICP).
7761   Note: It assumes you have set rho0=rhoConst=density of fresh water.   Note: It assumes you have set rho0=rhoConst=density of fresh water.
7762    
7763  checkpoint46g_post  checkpoint46g_post (2002/09/18)
7764  o Include a new diagnostic variable phiHydLow for the ocean model  o Include a new diagnostic variable phiHydLow for the ocean model
7765    - in z-coordinates, it is the bottom pressure anomaly    - in z-coordinates, it is the bottom pressure anomaly
7766    - in p-coordinates, it is the sea surface elevation    - in p-coordinates, it is the sea surface elevation
# Line 1130  o cleaned up find_rho Line 7778  o cleaned up find_rho
7778    - removed obsolete 'eqn' from the parameter list.    - removed obsolete 'eqn' from the parameter list.
7779  o added two new verification experiments: gop and goz  o added two new verification experiments: gop and goz
7780    (4x4 degree global ocean, 15 layers in pressure and height coordinates)    (4x4 degree global ocean, 15 layers in pressure and height coordinates)
7781  checkpoint46g_pre  checkpoint46g_pre (2002/09/16)
7782    
7783  checkpoint46f_post  checkpoint46f_post (2002/09/16)
7784  o Enable tangent linear (forward mode) gradient checks:  o Enable tangent linear (forward mode) gradient checks:
7785    - extended active file handling to g_... files    - extended active file handling to g_... files
7786    - added TANGENT_SIMULATION to theSimulationMode    - added TANGENT_SIMULATION to theSimulationMode
# Line 1140  o Enable tangent linear (forward mode) g Line 7788  o Enable tangent linear (forward mode) g
7788  o added tangent linear setup in verification/carbon/code_ftl  o added tangent linear setup in verification/carbon/code_ftl
7789  o added adjoint setup in verification/front_relax/code_ad  o added adjoint setup in verification/front_relax/code_ad
7790    
7791  checkpoint46e_post  checkpoint46e_post (2002/09/05)
7792  o Added new equation of state -> MDJWF  o Added new equation of state -> MDJWF
7793    - EOS of McDougall et al., 2002, JAOT, submitted    - EOS of McDougall et al., 2002, JAOT, submitted
7794    - caveat: the equation of state is only valid for a smaller (more    - caveat: the equation of state is only valid for a smaller (more
# Line 1149  o Added new equation of state -> MDJWF Line 7797  o Added new equation of state -> MDJWF
7797    - added more check values for density in check_eos (ini_eos.F), some of    - added more check values for density in check_eos (ini_eos.F), some of
7798      the old check values are out of the range of the MDJWF-eos, so don't      the old check values are out of the range of the MDJWF-eos, so don't
7799      expect perfect matches for those      expect perfect matches for those
7800  checkpoint46e_pre  checkpoint46e_pre (2002/08/19)
7801    
7802  checkpoint46d_post  checkpoint46d_post (2002/08/19)
7803  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
7804    'OCEANICP', also initialised field pressure correctly in ini_eos in the    'OCEANICP', also initialised field pressure correctly in ini_eos in the
7805    case of pressure coordinates. eosType='JMD95Z' in    case of pressure coordinates. eosType='JMD95Z' in
7806    combination with buoyancyRelation='OCEANICP' now causes an error.    combination with buoyancyRelation='OCEANICP' now causes an error.
7807  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
7808    in find_alpha/beta.    in find_alpha/beta.
7809  checkpoint46d_pre  checkpoint46d_pre (2002/08/15)
7810    
7811  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
7812    so that JMD95Z and JMD95P give approptiate static stability in find_rho.    so that JMD95Z and JMD95P give approptiate static stability in find_rho.
7813    
7814  checkpoint46c_post  checkpoint46c_post (2002/08/15)
7815  o Changes necessary for ocean in p-coordinates  o Changes necessary for ocean in p-coordinates
7816   -  Added new buoyancy relation = 'OCEANICP'   -  Added new buoyancy relation = 'OCEANICP'
7817   -  Added new parameters = gravitySign (this used to be contained inside   -  Added new parameters = gravitySign (this used to be contained inside
7818      the factor dRdZ which I added when we first switched to R coordinates).      the factor dRdZ which I added when we first switched to R coordinates).
7819   X GM/Redi is not compatible (yet)   X GM/Redi is not compatible (yet)
7820   X bottom drag and no-slip need to be debugged.   X bottom drag and no-slip need to be debugged.
7821  checkpoint46c_pre  checkpoint46c_pre (2002/08/07)
7822    
7823  checkpoint46b_post  checkpoint46b_post (2002/08/07)
7824  o Added new equation of state -> JMD95Z and JMD95P  o Added new equation of state -> JMD95Z and JMD95P
7825    - EOS of Jackett and McDougall, 1995, JAOT    - EOS of Jackett and McDougall, 1995, JAOT
7826    - moved all EOS parameters into EOS.h    - moved all EOS parameters into EOS.h
# Line 1181  o Added UNESCO EOS, but not recommended Line 7829  o Added UNESCO EOS, but not recommended
7829    in-situ temperature (see JMD95)    in-situ temperature (see JMD95)
7830  o Modified formatting for knudsen2.f in utils/knudsen2 and added  o Modified formatting for knudsen2.f in utils/knudsen2 and added
7831    unesco.f to be used with POLY3    unesco.f to be used with POLY3
7832  checkpoint46b_pre  checkpoint46b_pre (2002/07/31)
7833    
7834  checkpoint46a_post  checkpoint46a_post (2002/07/31)
7835  o Added (atmospheric) pressure loading  o Added (atmospheric) pressure loading
7836    - new field in FFIELDS.h, etc...    - new field in FFIELDS.h, etc...
7837    - new cpp flag ATMOSPHERIC_LOADING    - new cpp flag ATMOSPHERIC_LOADING
7838  o Changed hFacC to _hFacC in calc_phi_hyd.F  o Changed hFacC to _hFacC in calc_phi_hyd.F
7839  o Added SHORTWAVE_HEATING to some files for consistency  o Added SHORTWAVE_HEATING to some files for consistency
7840  checkpoint46a_pre  checkpoint46a_pre (2002/07/13)
7841    
7842  checkpoint46  checkpoint46 (2002/07/13)
7843  further merges from release1_p5  further merges from release1_p5
7844  o new ctrl package  o new ctrl package
7845    - adopted from ECCO environment to enable optimization    - adopted from ECCO environment to enable optimization
# Line 1218  o added hooks for Eliassen Palm fluxes ( Line 7866  o added hooks for Eliassen Palm fluxes (
7866  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
7867  o incorporated hooks for sponge layer code (external_forcing.F)  o incorporated hooks for sponge layer code (external_forcing.F)
7868    
7869  checkpoint45d_post  checkpoint45d_post (2002/07/12)
7870  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
7871  o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S  o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
7872    (affects plume_on_slope "cg2d" output)    (affects plume_on_slope "cg2d" output)
# Line 1232  o add new flags: Line 7880  o add new flags:
7880   - for each tracer, define internal flag for multiDimAdvection & A-B   - for each tracer, define internal flag for multiDimAdvection & A-B
7881  o monitor: change definition of KE to check conservation of Energy  o monitor: change definition of KE to check conservation of Energy
7882    
7883  checkpoint45c_post  checkpoint45c_post (2002/05/30)
7884  o Removed f90 comments ("!")  o Removed f90 comments ("!")
7885  o Modified initialisations to enable exf package for MITgcm  o Modified initialisations to enable exf package for MITgcm
7886    (without invoking ECCO_PACKAGE).    (without invoking ECCO_PACKAGE).
# Line 1240  o modifications to gradient check packag Line 7888  o modifications to gradient check packag
7888    - enable centered differences    - enable centered differences
7889    - modified format of standard output    - modified format of standard output
7890    
7891  checkpoint45b_post  checkpoint45b_post (2002/05/30)
7892  o cleaned exchange calls in cg2d  o cleaned exchange calls in cg2d
7893  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
7894  o included CPP option SINGLE_LAYER_MODE in thermodynamics  o included CPP option SINGLE_LAYER_MODE in thermodynamics
# Line 1252  o in initialise_varia, moved call packag Line 7900  o in initialise_varia, moved call packag
7900    (corresponding adjustment of TAF tape initialisation).    (corresponding adjustment of TAF tape initialisation).
7901  o in calc_diffusivity/calc_viscosity extended domain to full overlap.  o in calc_diffusivity/calc_viscosity extended domain to full overlap.
7902    
7903  checkpoint45a_post  checkpoint45a_post (2002/05/01)
7904  o compute Rho over the whole domain (extend iMin,jMin indices)  o compute Rho over the whole domain (extend iMin,jMin indices)
7905  o specific exchange for X-slice domain (case Ny=1)  o specific exchange for X-slice domain (case Ny=1)
7906  o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code  o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
# Line 1272  o errorMessageUnit set non-equal zero in Line 7920  o errorMessageUnit set non-equal zero in
7920    (conflict on some platforms, e.g. IBM SP3)    (conflict on some platforms, e.g. IBM SP3)
7921  o modified carbon verif.  o modified carbon verif.
7922    
7923  checkpoint44h_pre  checkpoint44h_pre (2002/03/14)
7924  o vertical grid option: allow to put the Interface at the middle between  o vertical grid option: allow to put the Interface at the middle between
7925    2 cell-centers ; replace delZ in pkg/kpp by drF.    2 cell-centers ; replace delZ in pkg/kpp by drF.
7926  o GM Advective form: Tracers are advected using the residual transport (=  o GM Advective form: Tracers are advected using the residual transport (=
7927    Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.    Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
7928    
7929  checkpoint44g_post  checkpoint44g_post (2002/03/05)
7930  o fix surface correction term in multiDimAdvection (affects plume_on_slope  o fix surface correction term in multiDimAdvection (affects plume_on_slope
7931    results) ; ifdef missing in thermodynamics.F    results) ; ifdef missing in thermodynamics.F
7932    
# Line 1343  o merge of relevant stuff from the ecco- Line 7991  o merge of relevant stuff from the ecco-
7991  o check parameters & config (chkpt44a_pre,post)  o check parameters & config (chkpt44a_pre,post)
7992  o OBC and NonLin_FrSurf.  o OBC and NonLin_FrSurf.
7993    
7994  checkpoint44  checkpoint44 (2002/01/18)
7995  o fix bug in mom_vi_del2uv  o fix bug in mom_vi_del2uv
7996  o select when filters are applied ; add options to zonal_filter (data.zonfilt)  o select when filters are applied ; add options to zonal_filter (data.zonfilt)
7997  o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)  o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
# Line 1351  o update AIM experiments (NCEP input fil Line 7999  o update AIM experiments (NCEP input fil
7999  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
8000  o added some stuff for AD  o added some stuff for AD
8001    
8002  checkpoint43  checkpoint43 (2001/09/28)
8003  o added two new advection tests  o added two new advection tests
8004  o added global 4x4 degree ocean test  o added global 4x4 degree ocean test
8005  o added test of H&S94 with free surface on cube  o added test of H&S94 with free surface on cube
8006  o some final mods for gradient check, adjoint,...  o some final mods for gradient check, adjoint,...
8007    
8008  checkpoint42  checkpoint42 (2001/09/27)
8009    Fixed AD-related problems:    Fixed AD-related problems:
8010  o Store directives up-to-date with re-arranged Adams-Bashforth  o Store directives up-to-date with re-arranged Adams-Bashforth
8011    (mainly thermodynamics.F)    (mainly thermodynamics.F)
# Line 1369  o Modified store directives for split of Line 8017  o Modified store directives for split of
8017    for the case ALLOW_KPP    for the case ALLOW_KPP
8018  o Cleaned argument list for timestep_tracer.F  o Cleaned argument list for timestep_tracer.F
8019    
8020  checkpoint41  checkpoint41 (2001/09/27)
8021  o re-formatted/added comments in prologues of key subroutines  o re-formatted/added comments in prologues of key subroutines
8022    to work with protex    to work with protex
8023    
8024  checkpoint40  checkpoint40 (2001/09/27)
8025  o moved calc_gs, calc_gt and calc_tr1 back to model/src  o moved calc_gs, calc_gt and calc_tr1 back to model/src
8026  o added FLT (floats) package from Arne along with demo. experiment  o added FLT (floats) package from Arne along with demo. experiment
8027  o re-arranged Adams-Bashforth scheme for tracers to allow easier  o re-arranged Adams-Bashforth scheme for tracers to allow easier
# Line 1382  o more mods for non-linear free-surface Line 8030  o more mods for non-linear free-surface
8030  o modified multi-dim method to work on cube  o modified multi-dim method to work on cube
8031  o bug fix in KPP (from DM)  o bug fix in KPP (from DM)
8032    
8033  checkpoint40pre9  checkpoint40pre9 (2001/09/27)
8034  o added DST advection schemes  o added DST advection schemes
8035  o fix MPI bug on SGI's  o fix MPI bug on SGI's
8036  o modifications for non-linear free-surface  o modifications for non-linear free-surface
# Line 1392  o changes to commenting of arguments for Line 8040  o changes to commenting of arguments for
8040  o added/updated many matlab scripts  o added/updated many matlab scripts
8041  o added multi-dimensional advection method for tracers  o added multi-dimensional advection method for tracers
8042        
8043  checkpoint40pre8  checkpoint40pre8 (2001/09/05)
8044  o new package rw/  o new package rw/
8045    Added method for dumping intermediate local arrays:    Added method for dumping intermediate local arrays:
8046    mdsio_writetile - same as mdsio_writefield except works from inside    mdsio_writetile - same as mdsio_writefield except works from inside
# Line 1411  o TAMC-related update to cope with mom_f Line 8059  o TAMC-related update to cope with mom_f
8059    currently nothing implemented to switch this storing off    currently nothing implemented to switch this storing off
8060    in case fluxform is used since no CPP flag available).    in case fluxform is used since no CPP flag available).
8061    
8062  checkpoint40pre7  checkpoint40pre7 (2001/08/14)
8063  o bug fix in dynamics.F  o bug fix in dynamics.F
8064    calc_viscosity called before k=1,Nr loop.    calc_viscosity called before k=1,Nr loop.
8065  o added some #ifdef's ALLOW_PASSIVE_TRACER  o added some #ifdef's ALLOW_PASSIVE_TRACER
8066  o cleaned initialisations in ctrl_map_ini  o cleaned initialisations in ctrl_map_ini
8067    related to TAF    related to TAF
8068    
8069  checkpoint40pre6  checkpoint40pre6 (2001/08/13)
8070  o split dynamics into thermodynamics & dynamics  o split dynamics into thermodynamics & dynamics
8071  o corresponding split of calc_diffusivity into  o corresponding split of calc_diffusivity into
8072    calc_diffusivity, calc_viscosity    calc_diffusivity, calc_viscosity
# Line 1426  o corresponding split of calc_diffusivit Line 8074  o corresponding split of calc_diffusivit
8074  o Added diffkr, kapgm to control variables  o Added diffkr, kapgm to control variables
8075  o bug fix in gmredi_slope_limit for ldd97  o bug fix in gmredi_slope_limit for ldd97
8076    
8077  checkpoint40pre5  checkpoint40pre5 (2001/07/31)
8078  o proper initialization of Adams-Bashforth time stepping  o proper initialization of Adams-Bashforth time stepping
8079    + uses forward step for very first step of model (iter=0)    + uses forward step for very first step of model (iter=0)
8080  o re-generated *all* output since almost all output is modified by this  o re-generated *all* output since almost all output is modified by this
# Line 1440  o added new expt "solid-body.cs-32x32x1" Line 8088  o added new expt "solid-body.cs-32x32x1"
8088    + this uses an alternative form of ini_curvilinear_grid.F which    + this uses an alternative form of ini_curvilinear_grid.F which
8089      is not necessarily any better than the current one...      is not necessarily any better than the current one...
8090    
8091  checkpoint40pre4  checkpoint40pre4 (2001/07/30)
8092  o added re-initialisations of utrans,vtrans,rtrans in  o added re-initialisations of utrans,vtrans,rtrans in
8093    calc_common_factors which are crucial for TAF.    calc_common_factors which are crucial for TAF.
8094  o extended iMin,jMin range for calc_common_factors,  o extended iMin,jMin range for calc_common_factors,
# Line 1448  o extended iMin,jMin range for calc_comm Line 8096  o extended iMin,jMin range for calc_comm
8096  o added option ALLOW_PASSIVE_TRACER  o added option ALLOW_PASSIVE_TRACER
8097  o a few minor updates and fixes  o a few minor updates and fixes
8098    
8099  checkpoint40pre3  checkpoint40pre3 (2001/07/13)
8100  o created calc_gtr1.F for gad package  o created calc_gtr1.F for gad package
8101  o split the_main_loop and re-introduced forward_step  o split the_main_loop and re-introduced forward_step
8102  o some recomputations of nIter0 for TAMC  o some recomputations of nIter0 for TAMC
8103    
8104  checkpoint40pre2  checkpoint40pre2 (2001/07/13)
8105  o Updated to latest branch of AJA, JMC  o Updated to latest branch of AJA, JMC
8106  o Added gradient check package  o Added gradient check package
8107  o Added routines for passive tracer handling  o Added routines for passive tracer handling
8108  o Added carbon sequestration sensitivity experiment  o Added carbon sequestration sensitivity experiment
8109    
8110  checkpoint39  checkpoint39 (2001/05/14)
8111   o Modifications and fixes to support TAMC   o Modifications and fixes to support TAMC
8112     (mainly missing or wrong directives)     (mainly missing or wrong directives)
8113   o Corrected common blocks when fooling TAMC to produce adjoint I/O   o Corrected common blocks when fooling TAMC to produce adjoint I/O
# Line 1473  checkpoint39 Line 8121  checkpoint39
8121           (NB: this is not the full ECCO environment)           (NB: this is not the full ECCO environment)
8122   o disabled some packages by default in genmake   o disabled some packages by default in genmake
8123    
8124  checkpoint38  checkpoint38 (2001/04/10)
8125   o see notes_c37_adj.txt   o see notes_c37_adj.txt
8126   o corrected wrong layer index in external_forcing_t   o corrected wrong layer index in external_forcing_t
8127   o replaced the_main_loop/forward_step by the_main_loop   o replaced the_main_loop/forward_step by the_main_loop
# Line 1481  checkpoint38 Line 8129  checkpoint38
8129     (replaced criteria for initial/final state)     (replaced criteria for initial/final state)
8130   o added runtime flag for pre-C35 pickups: usePickupBeforeC35   o added runtime flag for pre-C35 pickups: usePickupBeforeC35
8131    
8132  checkpoint37  checkpoint37 (2001/03/13)
8133   o mdsio.F routine split and packaged in pkg/mdsio   o mdsio.F routine split and packaged in pkg/mdsio
8134     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
8135      used unless genmake -disable=mdsio)      used unless genmake -disable=mdsio)
# Line 1498  checkpoint37 Line 8146  checkpoint37
8146   o Non-Hydrostatic pickup file Pb fixed.   o Non-Hydrostatic pickup file Pb fixed.
8147   o bug with Rigid-lid version (since c35) fixed.     o bug with Rigid-lid version (since c35) fixed.  
8148    
8149  checkpoint36  checkpoint36 (2001/02/20)
8150   o implement Crank-Nickelson barotropic time-stepping   o implement Crank-Nickelson barotropic time-stepping
8151   o recover Time-Average diagnostics   o recover Time-Average diagnostics
8152   o fix Pb in checkpoint (PR#19)   o fix Pb in checkpoint (PR#19)
8153   o AIM become a standard package ; clean unused CPP_kees   o AIM become a standard package ; clean unused CPP_kees
8154    
8155  checkpoint35  checkpoint35 (2001/02/08)
8156   o subtantial rewrite of dynamics.f   o subtantial rewrite of dynamics.f
8157   o allows staggered time-stepping   o allows staggered time-stepping
8158   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
8159   o added bottom drag (linear + quadratic)   o added bottom drag (linear + quadratic)
8160    
8161  checkpoint34  checkpoint34 (2001/01/30)
8162   o Modified exchange routines for correct reverse simulation.   o Modified exchange routines for correct reverse simulation.
8163   o Added verification output to comply with bug fix in impldiff.F   o Added verification output to comply with bug fix in impldiff.F
8164     as of c33 (exp2, natl_box).     as of c33 (exp2, natl_box).
# Line 1521  checkpoint34 Line 8169  checkpoint34
8169   o Added routine GLOBAL_SUM_INT to global_sum.F   o Added routine GLOBAL_SUM_INT to global_sum.F
8170   o Added mdsio_gl.F for ECCO purposes.   o Added mdsio_gl.F for ECCO purposes.
8171    
8172  checkpoint33  checkpoint33 (2000/11/30)
8173   o Fixed bug in lower BC in impldiff.F   o Fixed bug in lower BC in impldiff.F
8174   o Fixed confusion about units of forcing arrays in FFIELDS.h   o Fixed confusion about units of forcing arrays in FFIELDS.h
8175     namely Fu,Fv,Qnet,Qsw,EmPmR:     namely Fu,Fv,Qnet,Qsw,EmPmR:
# Line 1539  checkpoint33 Line 8187  checkpoint33
8187       possibly use them.       possibly use them.
8188   o Corrected genmake to delete a temporary file during configuration   o Corrected genmake to delete a temporary file during configuration
8189    
8190  checkpoint32  checkpoint32 (2000/11/13)
8191   o Scaling of forcing fields moved from external_forcing.F to   o Scaling of forcing fields moved from external_forcing.F to
8192     external_fields_scale.F, called directly after loading fields.     external_fields_scale.F, called directly after loading fields.
8193   o Surface relaxation terms added to surface tendency fields in   o Surface relaxation terms added to surface tendency fields in
# Line 1550  checkpoint32 Line 8198  checkpoint32
8198   o Modifications and bug fixes in KPP package.   o Modifications and bug fixes in KPP package.
8199   o Verification experiment for KPP added (verification/nat_box/)   o Verification experiment for KPP added (verification/nat_box/)
8200    
8201  checkpoint31  checkpoint31 (2000/09/11)
8202   o Packages interface brought in line with defined standard   o Packages interface brought in line with defined standard
8203     -> new routines packages_...F     -> new routines packages_...F
8204     -> changes in initialise_fixed.F, initialise_varia.F     -> changes in initialise_fixed.F, initialise_varia.F
# Line 1567  checkpoint31 Line 8215  checkpoint31
8215     - not yet tested for GMRedi.     - not yet tested for GMRedi.
8216     - not yet tested for KPP.     - not yet tested for KPP.
8217    
8218  checkpoint30  checkpoint30 (2000/07/13)
8219   o Updates for OBCs   o Updates for OBCs
8220   o New experiment for test OBCs (internal_wave)   o New experiment for test OBCs (internal_wave)
8221   o New output.txt in verification/exp4/results/   o New output.txt in verification/exp4/results/
# Line 1576  checkpoint30 Line 8224  checkpoint30
8224   o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)   o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
8225     and entry for T90 in genmake     and entry for T90 in genmake
8226    
8227  checkpoint29  checkpoint29 (2000/06/21)
8228   o packaged KPP and GM/Redi   o packaged KPP and GM/Redi
8229    
8230  checkpoint28  checkpoint28 (2000/06/09)
8231   o Corrected initialization of hFacMin for difference vertical coordinates   o Corrected initialization of hFacMin for difference vertical coordinates
8232   o Modified calculation of partial cell thickness to more robust algorithm   o Modified calculation of partial cell thickness to more robust algorithm
8233   o config_summary.F: replaced write_1D_... by write_0D_...   o config_summary.F: replaced write_1D_... by write_0D_...
# Line 1592  checkpoint28 Line 8240  checkpoint28
8240     included store directives and tape key computations required for TAMC.     included store directives and tape key computations required for TAMC.
8241   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
8242    
8243  checkpoint27  checkpoint27 (2000/04/10)
8244   o fixed calc_isoslopes() to so that cancellation of terms in tensor   o fixed calc_isoslopes() to so that cancellation of terms in tensor
8245     formulation works properly with variable resolution.     formulation works properly with variable resolution.
8246   o restructured the calling tree between the_model_main() and dynamics()   o restructured the calling tree between the_model_main() and dynamics()
# Line 1600  checkpoint27 Line 8248  checkpoint27
8248   o introduced initialization file pSurfInitFile for free surface (cg2d_x)   o introduced initialization file pSurfInitFile for free surface (cg2d_x)
8249     in new routine ini_psurf()     in new routine ini_psurf()
8250    
8251  checkpoint26  checkpoint26 (2000/04/05)
8252   o moved some #ifdef in optional routines to encompass everything   o moved some #ifdef in optional routines to encompass everything
8253     except the argument declarations. This was using up some memory.     except the argument declarations. This was using up some memory.
8254   o fixed macros like _ADT to work with both versions of Linux cpp   o fixed macros like _ADT to work with both versions of Linux cpp
# Line 1610  checkpoint26 Line 8258  checkpoint26
8258     (macros are now in eesupp/inc/CPP_EEMACROS.h)     (macros are now in eesupp/inc/CPP_EEMACROS.h)
8259   o patch for 2 processor JAM mode   o patch for 2 processor JAM mode
8260    
8261  checkpoint25  checkpoint25 (2000/03/15)
8262   o updates for OBCs and NH   o updates for OBCs and NH
8263   o dramatically reduced memory usage   o dramatically reduced memory usage
8264   o added "JAM" routines for use on Artic network   o added "JAM" routines for use on Artic network
# Line 1621  checkpoint25 Line 8269  checkpoint25
8269      an explicit free-surface option)      an explicit free-surface option)
8270   o initial state input files for U and V   o initial state input files for U and V
8271    
8272  checkpoint24  checkpoint24 (1999/08/02)
8273   o Removed some spurious "REAL"s   o Removed some spurious "REAL"s
8274   o Updated KPP to latest version from JPL   o Updated KPP to latest version from JPL
8275   o Added a COS(latitude) in horizontal viscosity   o Added a COS(latitude) in horizontal viscosity
8276    
8277  checkpoint23  checkpoint23 (1999/05/26)
8278   o Added del^4 diffusion for salt and temperature   o Added del^4 diffusion for salt and temperature
8279   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
8280    
8281  checkpoint22  checkpoint22 (1999/05/18)
8282   o Made many small changes: implicit none, format(i5), etc...   o Made many small changes: implicit none, format(i5), etc...
8283   o Introduced KPP mixing scheme (compiles and runs but *not* tested)   o Introduced KPP mixing scheme (compiles and runs but *not* tested)
8284    
8285  checkpoint21  checkpoint21 (1999/05/18)
8286   o Introduced new I/O package that supports direct-access records (mdsio.F)   o Introduced new I/O package that supports direct-access records (mdsio.F)
8287   o Split-up mid-level I/O routines   o Split-up mid-level I/O routines
8288   o Updated input data for experiments 0,1,2,4 and 5   o Updated input data for experiments 0,1,2,4 and 5
8289   o Finally removed the genmake.* scripts (everyone seems happy with genmake)   o Finally removed the genmake.* scripts (everyone seems happy with genmake)
8290    
8291  checkpoint20  checkpoint20 (1999/03/22)
8292   o Tidied up open-boundaries some more   o Tidied up open-boundaries some more
8293   o Added non-hydrostatic code   o Added non-hydrostatic code
8294   o Fixed some input data   o Fixed some input data
8295   o Modified MPI start-up to work in "coupled" context.   o Modified MPI start-up to work in "coupled" context.
8296    
8297  checkpoint19  checkpoint19 (1998/12/15)
8298   o Tidied up directory structure for verification experiments.   o Tidied up directory structure for verification experiments.
8299   o Added new code for open boundaries.   o Added new code for open boundaries.
8300   o Corrected advective terms near boundaries.   o Corrected advective terms near boundaries.
# Line 1654  checkpoint19 Line 8302  checkpoint19
8302   o Implemented free-slip/no-slip BCs and del^4 dissipation.   o Implemented free-slip/no-slip BCs and del^4 dissipation.
8303   o Split default parameters out of ini_parms.F into set_defaults.F.   o Split default parameters out of ini_parms.F into set_defaults.F.
8304    
8305  checkpoint18  checkpoint18 (1998/11/30)
8306   o Further changes for optional code generation with   o Further changes for optional code generation with
8307     CPP - ugh!     CPP - ugh!
8308    
8309  checkpoint17  checkpoint17 (1998/11/03)
8310   o Beginning to incorporating modularity   o Beginning to incorporating modularity
8311     for supporting atmos. and ocean configs.     for supporting atmos. and ocean configs.
8312   o Small changes for TAMC complinace   o Small changes for TAMC complinace
8313   o New ultra simple test case. Barotropic box   o New ultra simple test case. Barotropic box
8314     configuration "exp0".     configuration "exp0".
8315    
8316  checkpoint16  checkpoint16 (1998/10/28)
8317   o Minor changes to exchange routines to support   o Minor changes to exchange routines to support
8318     accumulation in reverse mode. Adjoint of an     accumulation in reverse mode. Adjoint of an
8319     assignment is an addition.     assignment is an addition.
# Line 1673  checkpoint16 Line 8321  checkpoint16
8321     syntax) and by g77 under Linux ( 72 character     syntax) and by g77 under Linux ( 72 character
8322     limit ).     limit ).
8323    
8324  checkpoint15  checkpoint15 (1998/09/29)
8325   Rewrote exchange routines to allow   Rewrote exchange routines to allow
8326   o General tile <-> tile connectivity.   o General tile <-> tile connectivity.
8327   o TAMC reverse mode flag ( is this really needed? )   o TAMC reverse mode flag ( is this really needed? )
# Line 1682  checkpoint15 Line 8330  checkpoint15
8330     shmput/shmget, VIA, SYSV shmem and every other cool     shmput/shmget, VIA, SYSV shmem and every other cool
8331     communication method.     communication method.
8332    
8333  checkpoint14  checkpoint14 (1998/09/09)
8334   Consistent isomorphism chages made. These allow dynamical core   Consistent isomorphism chages made. These allow dynamical core
8335   to support both pressure and meters as a vertical coordinate.   to support both pressure and meters as a vertical coordinate.
8336    
8337  checkpoint13  checkpoint13 (1998/07/17)
8338   Release which corrects global_max problem and a couple   Release which corrects global_max problem and a couple
8339   of KGM time-averaging diagnostic errors. Also contains   of KGM time-averaging diagnostic errors. Also contains
8340   a double-gyre experiment setup as well as the baseline   a double-gyre experiment setup as well as the baseline
# Line 1701  branch-point-rdot Line 8349  branch-point-rdot
8349   I don't want to commit the rDot to the main-trunk until   I don't want to commit the rDot to the main-trunk until
8350   we've actually tested it...   we've actually tested it...
8351    
8352  checkpoint12  checkpoint12 (1998/07/08)
8353   Tidy up and added generic genmake script (formerly   Tidy up and added generic genmake script (formerly
8354   configure script).   configure script).
8355   Released to testers.   Released to testers.
8356    
8357  checkpoint11  checkpoint11 (1998/07/02)
8358   Re-arranged initialise() and introduced ini_vertical_grid()   Re-arranged initialise() and introduced ini_vertical_grid()
8359   and ini_masks_etc().   and ini_masks_etc().
8360    
8361  checkpoint10  checkpoint10 (1998/07/01)
8362   Introduced the configure script.   Introduced the configure script.
8363   Separated out the diags package.   Separated out the diags package.
8364   Added template for writing time-averages of tile/intermediate quantities.   Added template for writing time-averages of tile/intermediate quantities.
8365   Updated SIZE.h in exp2 and made the data big-endian.   Updated SIZE.h in exp2 and made the data big-endian.
8366    
8367  checkpoint9  checkpoint9 (1998/06/22)
8368   MPI fix. Filename changes (meta/data). salbin*y stuff.   MPI fix. Filename changes (meta/data). salbin*y stuff.
8369   General tidy-up.   General tidy-up.
8370   SST.bin SSS.bin added to verification/exp2   SST.bin SSS.bin added to verification/exp2
8371    
8372  checkpoint8  checkpoint8 (1998/06/22)
8373   Inludes time-dependant forcing and time-averaging.   Inludes time-dependant forcing and time-averaging.
8374   Works at 4x4 and 2.8125x2.8125 global   Works at 4x4 and 2.8125x2.8125 global
8375    
# Line 1731  checkpoint7-4degree-ref Line 8379  checkpoint7-4degree-ref
8379   model etc..   model etc..
8380   Configured for verification/exp2 - 4 degree global, two process.   Configured for verification/exp2 - 4 degree global, two process.
8381    
8382  checkpoint7  checkpoint7 (1998/06/15)
8383   Created by cnh   Created by cnh
8384   Simple 4 degree global simulation   Simple 4 degree global simulation
8385   configuration.   configuration.
# Line 1739  checkpoint7 Line 8387  checkpoint7
8387   hydrography, bathymetry etc   hydrography, bathymetry etc
8388   Does not include Heat Flux and E-P   Does not include Heat Flux and E-P
8389    
8390  checkpoint6  checkpoint6 (1998/06/08)
8391   Created by cnh   Created by cnh
8392   merged checkpoint5 with CD and   merged checkpoint5 with CD and
8393   spherical polar code.   spherical polar code.
8394   Still some problems with GM Redi   Still some problems with GM Redi
8395   abd full topography.   abd full topography.
8396    
8397  checkpoint5  checkpoint5 (1998/06/08)
8398   Created by AJA   Created by AJA
8399   contains updates to GM Redi   contains updates to GM Redi
8400   and reordered timestepping loop   and reordered timestepping loop
8401   for Implicit Diffusion.   for Implicit Diffusion.
8402    
8403  checkpoint4  checkpoint4 (1998/05/30)
8404   Created by cnh   Created by cnh
8405   Contains memory saving macros ( _rdxc etc..) for when   Contains memory saving macros ( _rdxc etc..) for when
8406   grid variations are limited.   grid variations are limited.
8407   Contains polynomial coeffs for EOS and knudsen program   Contains polynomial coeffs for EOS and knudsen program
8408   for generation.   for generation.
8409    
8410  checkpoint3  checkpoint3 (1998/05/26)
8411   Created by cnh   Created by cnh
8412   Added extra flags for runtime options   Added extra flags for runtime options
8413   Added this file   Added this file

Legend:
Removed from v.1.297  
changed lines
  Added in v.1.1912

  ViewVC Help
Powered by ViewVC 1.1.22