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revision 1.1794 by jmc, Thu Dec 27 20:09:11 2012 UTC revision 1.1918 by jmc, Mon Aug 26 13:03:07 2013 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint64n (2013/08/26)
8    o verification/halfpipe_streamice:
9      - change to matrix construction; update both Fwd & AD output.
10    o verification/tutorial_tracer_adjsens:
11      - OpenAD test: switch to vector-invariant momentum since fluxform with
12        rStar causes problems with OpenAD; update output.
13    o tools:
14      - genmake2: define a common prefix for all temp-file names ; move them
15        to local /tmp disk (but would be easy to move them back);
16      - xmakedepend: apply the same switch for temp-files.
17    o pkg/offline:
18      - changes for use with rStar (NLFS): assume that we continue to provide
19        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
20        output files) and apply r* scaling at each time-step (function of the time
21        varying Eta field); use normal pickup files (needed for restart with NLFS).
22    o adjoint with OpenAD:
23      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
24        package openad.  This package has to be compiled for all runs with OpenAD
25        instead of specifying code_oad_all as a modification directory.
26      - link the fortran templates from tools/OAD_support to the build directory
27        for preprocessing to avoid conflicts between different setups compiled
28        simultaneously and simplify cleanup.
29    o pkg/exf:
30      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
31        main model or other pkgs are exchanged in EXF_MAPFIELDS).
32    o model/src:
33      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
34        (similar to do_fields_blocking_exchanges.F).
35    o tools/genmake2:
36      - remove TAF output src code just before calling staf (when not doing a fresh
37        built, will stop if things go wrong with staf).
38      - fix target "adobj" (left from TAF version-2 transition)
39    o pkg/diagnostics:
40      - add a parameter to track the status of pkg/diagnostics activation;
41        this replace/extend the use of logical param "settingDiags" (to check
42        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
43        New S/R to print error message and stop when pkgStatus is not right.
44      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
45    
46    checkpoint64m (2013/08/13)
47    o model/inc:
48      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
49        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
50    o pkg/kpp & aim_v23:
51      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
52    o pkg/seaice:
53      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
54        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
55      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
56    o eesupp/src:
57      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
58        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
59    o switch to TAF version-2:
60      - add flow directives to "freeze" naming convention for ad-routines that
61        are used in I/O routines of adjoint state and associated common blocks
62        that are used in adcommon.h (backward compatible with version-1)
63      - update all ad-optfiles (in tools/adjoint_options + few local to some
64        verification exp) to switch to latest TAF version (currently 2.5.5);
65        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
66        out except for diva).
67      - the major change with TAF version-2 is that both the differentiated
68        routines and the forward routines (new) are returned as part of the TAF
69        output source code. Update genmake2 accordingly.
70      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
71        with version-2 when compared to TLM or FWD gradient); other experiments
72        output show minor changes (machine truncation level); update the few AD &
73        TLM output with 12 matching digits only (some prior to version-2 switch).
74    
75    checkpoint64l (2013/08/05)
76    o model/src:
77      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
78      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
79        when using TAF but only if using OpenAD.
80    o pkg/mom_common+fluxform+vecinv:
81      - always set horiz. viscosity arrays to background value before calling
82        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
83        only when using variable horiz. viscosity (useVariableVisc=T);
84      - simplify mom_vecinv.F (only 1 block for momViscosity).
85    o pkg/mom_common: variable horiz. viscosity in NH code
86      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
87        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
88      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
89        useBiharmonicVisc & useVariableVisc.
90      - fix old bug (already in 1rst implementation of variable horizontal viscosity
91        in calc_gw.F, version 1.27, 2006/06/20):
92        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
93        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
94      - change background horiz viscosity in vertical momentum (gW) to always be
95        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
96        any type of variable viscosity, e.g., viscAh/4Grid)
97      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
98        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
99        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
100        default viscAh,viscA4 is zero).
101    o model/src:
102      - extend length of drC & recip_drC from Nr to Nr+1.
103    o Divided Adjoint (DIVA) with MPI:
104      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
105      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
106        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
107    
108    checkpoint64k (2013/07/23)
109    o tools/OAD_support:
110      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
111        and remove it from genmake2.
112    o tools/build_options:
113      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
114        MPI_HEADER_FILES list (let genmake2 find the missing headers)
115    o verification/halfpipe_streamice:
116      - change to driving stress formulation; update both Fwd & AD output.
117    o tools/genmake2 and Divided Adjoint with MPI:
118      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
119      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
120      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
121        Makefile, which is set by genmake2, and check which mpi-headers are needed.
122        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
123      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
124    o testreport:
125      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
126        perform additional runs (number of additional runs is "add_DIVA_runs" taken
127        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
128    o verification/lab_sea (AD test):
129      - change to test Divided Adjoint Run in this set-up (both standard AD test
130        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
131    o pkg atm_ & ocn_compon_interf:
132      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
133        staggerTimeStep implementation) and disable (retired) corresponding
134        parameter.
135    o pkg/offline:
136      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
137      - add S/R OFFLINE_CHECK to print offline parameter summary
138        and stop if loading a file that is not used;
139      - enable to calculate GMRedi tensor, KPP mixing and convective index
140        when the corresponding file(s) is/are not specified (but pkg is used).
141      - comment out resetting of monitorFreq (to endTime) since it still useful
142        for monitoring CFL numbers and checking offline fields.
143    o OpenAD:
144      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
145        smaller standard output) and generate new (smaller) output (on baudelaire
146        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
147    o model/src:
148      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
149        (where external_forcing_adjust was called) and change list of arguments;
150      - merge external_forcing_adjust.F into external_forcing_surf.F
151      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
152        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
153        previously in file "balance_relax.F", now removed); remove corresponding
154        arrays in FFIELDS.h.
155      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
156        a hack for getting back surfaceForcingS (loaded from file) when using
157        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
158      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
159        (was getting only 11 digits for AD-grad, due to different truncation
160         error in AD code).
161    
162    checkpoint64j (2013/07/04)
163    o pkg/offline:
164      - to enable the use of other features with pkg offline (e.g., obcs),
165        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
166      - comment out "allowFreezing" (now active) in 2 offline testing exp.
167    o pkg/exf ALLOW_RUNOFTEMP
168      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
169      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
170      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
171    o pkg/atm_phys:
172      - allows to add some damping on uVel,vVel (strength only function of k).
173    o verification, ad-tests:
174      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
175        global_ocean_ebm and offline_exf_seaice.thsice.
176    o verification/halfpipe_streamice:
177      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
178        flux input boundary conditions to be ignored; a fix for this bug changed
179        verification results for forward test.
180      - add adjoint test.
181    o pkg/ptracers:
182      - allow to restart without SOM pickup (resetting SOM to zero).
183    o pkg/gmredi:
184      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
185      - It uses mixing length theory and suppression by steering level effects to
186        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
187        to JPO, for more details).
188      - It also uses the diffusivity to calculate an eddy induced streamfunction
189        based on a PV closure (rather than a buoyancy closure as in GM).
190      - New files added to pkg/gmredi:
191        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
192          induced overturning streamfunction (called from gmredi_calc_tensor)
193        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
194          for use in gmredi_k3d
195        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
196          the eddy diffusivity
197    
198    checkpoint64i (2013/06/18)
199    o pkg/cheapaml:
200      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
201        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
202        with pkg/cheapaml.
203    o utils/python: add subpackage for cubed sphere function, first example is
204        simple cs.pcol to plot 2D fields on a map
205    o pkg/streamice:
206      - This is a new package in MITgcm, which solves dynamic equations for ice
207         sheets and ice streams
208      - At the moment it is independent of atmosphere/ocean dynamics, or any
209        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
210        ed that this will change)
211      - There is a new verification exercise that tests it, halfpipe_streamice,
212        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
213        rectangular embayment
214      - halfpipe_streamice is forward-only for now, will have TAF test soon
215      - for questions, email dgoldber@mit.edu
216    o pkg/thsice:
217      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
218        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
219      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
220         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
221      - allow precip from pkg/cheapaml to make snow over seaice.
222    o pkg/cfc:
223      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
224      - remove atmos CFC 2-D arrays from common bloc (now local variables)
225      - change some hard-coded constant to run time parameter for reading and
226        and interpolating atmospheric CFC ; keep same default as previously.
227      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
228      - put arguments in standard order: myTime, myIter, myThid
229      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
230        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
231      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
232      - new routine to print summary of CFC params and check for consistency.
233    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
234      similar to thsice_advdiff.
235      Note that for the B-grid case the routine parameters uc/vc are overwritten.
236    o pkg/cfc:
237      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
238        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
239      - fix interpolation of atmphspheric CFC between Sorthern and Northern
240        hemisphere value.
241    o pkg/seaice:
242      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
243    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
244                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
245      - requires an additional time level that is stored in the pickup
246      - you can start with AB2 from a pickup without this time level with
247        pickupStrictlyMatch = .false.
248    
249    checkpoint64h (2013/05/26)
250    o pkg/cheapaml:
251      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
252        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
253      - consistent treatment of uWind,vWind location: assume everywhere in
254        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
255        (Note: was already the case for Tair,Qair advection);
256        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
257      - compute diabatic forcing only in the interior (excluding overlap regions)
258      - fill in array "Qsw" (for short-wave heating);
259      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
260        before any update (consistent with MITgcm state var diagnostics);
261      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
262        non periodic ; + adjusted for uWind,vWind (C-grid).
263    o pkg/seaice:
264      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
265        add explicitly pkg/exf in experiments that currently use pkg/seaice.
266      - allows to compile pkg/seaice without pkg/exf.
267    o tools/OAD_support:
268      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
269        of array "ourStepOf" in function rvNextAction (revolve.F90).
270    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
271      - change pkg name (to be used with other atmospheric physics pkg)
272        but by-pass CVS when making the new pkg so that we keep the CVS history.
273    o pkg/offline:
274      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
275        (previously called from pkg/dic_surfforcing_init.F)
276    o model/src:
277      - re-order sequence of calls within packages_init_variables.F, using
278        standard order, except for:
279         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
280         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
281    o new pkg: atm_phys
282      - add entry point and source code (previously in contrib
283          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
284        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
285      - re-order sequence of calls within packages_readparms.F,
286         packages_init_fixed.F and packages_write_pickup.F
287        (but skip packages_init_variables.F because of TAF issues).
288      - update contrib/*/atm_gray/ experiment.
289    o pkg/seaice (ITD code):
290      - simplify and fix the writing of pickup-files for ITD case
291    o pkg/seaice (ITD code):
292      - introduce floe size dependent lateral melt for ITD case;
293      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
294      - update seaice_itd experiment main output.
295    o pkg/thsice:
296      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
297        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
298        changed accordingly pkg/atm2d.
299    
300    checkpoint64g (2013/05/01)
301    o pkg/exf ALLOW_RUNOFTEMP
302      - if defined,  river and glacier runoff temperature can be read-in from
303        runoftempfile; runoftempfile needs to have same format as runofffile
304    o pkg/thsice (& pkg/bulk_force):
305      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
306        for energy content of Precip + RunOff & Evap (like with pkg/exf).
307      - change computation domain to always be the interior (without overlap).
308      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
309    o verification/tutorial_global_oce_biogeo:
310      - add preliminary OpenAD setup (still has problems)
311    o pkg/seaice:
312      - turn some parameters for choosing the convergence criterion of
313        the inexact Newton method (JFNK) into runtime parameters for convenience
314      - clean up seaice_calc_viscosities.F: remove/retire two options for
315        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
316        the results of lab_sea/input because a division has been replaced by
317        a multiplication with the reciprocal (sumNorm)
318      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
319        convergence of solver (changes results, of course), and to test some
320        new features
321    o model/src:
322      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
323      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
324      - move forcing adjustment (balancing surface forcing) in specific S/R
325        where might also be applied exchanges (if needed) to forcing arrays.
326    o pkg/shelfice:
327      - allow to specify the Ice-Shelf mass per unit area (instead of
328        shelficeLoadAnomaly) and do the conversion from one to the other
329      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
330        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
331        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
332        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
333      - update isomip experiment forward output (get machine truncation error
334        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
335    o verification/offline_exf_seaice:
336      revise data.seaice in input.thermo and input_ad and update results accordingly
337        HO = 0.2, SEAICE_areaLossFormula = 2,
338        SEAICE_growMeltByConv = .TRUE.,
339        SEAICE_doOpenWaterMelt = .TRUE.,
340      Improve consistency with input.thsice and fix the spurious 500m ice corners
341    o verification/global_ocean.cs32x15:
342      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
343        in icedyn (thsice+seaice-dyn) test and update output.
344    o verification/offline_exf_seaice:
345      - adjust list of tested variables (with testreport) and update
346        standard test output with better slection of monitored fields.
347    o pkg/cd_code:
348      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
349        experiment lab_sea.hb87
350    o tools/genmake2:
351      - change default makedepend from the system default to tools/xmakedepend:
352        When no makedepend is specified, select tools/xmakedepend it the test pass,
353        otherwise select the system default (if exist and pass the test) or
354        try to build cyrus-makedepend ; stop if none of the 3 works.
355    o pkg/exf & pkg/thsice:
356      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
357        for energy content of Precip + RunOff & Evap. Assumes:
358       1) Rain has same temp as Air.
359       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
360       3) Run-Off comes at the temp of surface water (with same Cp)
361       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
362        put directly into Latent Heat flux & should use water-vapor heat capacity.
363       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
364        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
365    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
366        (compile when SEAICE_ALLOW_JFNK is defined)
367    o pkg/thsice:
368      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
369        implementation): move THSICE_AVE call after the advection (called directly
370        from thsice_do_advect.F).
371    o verification/global_ocean.90x40x15 and OpenAD:
372      New experiment for OpenAD is identical to the one in input_ad except that
373        multiDimAdvection=.FALSE.,
374      There is still an issue with this.
375    o pkg/thsice:
376      - account for ice velocity (ocean relative velocity) in turbulent heat flux
377        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
378        and offline_exf_seaice (main test).
379    
380    checkpoint64f (2013/03/31)
381    o verification/OpenAD:
382      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
383    o verification/isomip, pkg/shelfice and OpenAD:
384      - add OpenAD setup to this exp and make shelfice package work with OpenAD
385    o verification/tutorial_global_oce_biogeo:
386      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
387    o verification/offline_exf_seaice:
388      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
389    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
390      - add OpenAD setup to this exp and make ptracers package work with OpenAD
391    o pkg/seaice/seaice_evp.F:
392       mask the asymmetric contribution of the ice-ocean stress (when
393       the turningAngle is non-zero) over open water to avoid stripes
394       in the EVP-solutions after many EVP-substeps. This does not change
395       the verification experiment (because turningAngle=0 in that experiment),
396       but will affect other EVP solutions with turningAngle.ne.0
397    o verification, AD & TLM output:
398      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
399        additions and multiplications which affect results at machine truncation
400        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
401        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
402        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
403        digits of matching.
404    o pkg/seaice:
405       modify lsr-algorithm so that it vectorizes AND converges by using a
406       "zebra" method: split vector loop into two with step size 2; this
407       solves a general convergence problem for the JFNK solver on a vector
408       computer. It has the potential to even improve convergence for
409       non-vector machines, but it does change the results so it is turned
410       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
411       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
412    
413    checkpoint64e (2013/03/05)
414    o pkg/ecco and several verification experiments:
415       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
416       from ecco package, and revert to unified routine in model/src/
417       Adjust verification experiments accordingly, especially gloal_oce_llc90
418       Should conclude long-standing work by Gael to reconsile the_main_loop with
419       ECCO and will enable OpenAD's revolve loop in ECCO setup.
420    o pkg/generic_advdiff:
421      - implement compressible flow method for multi-dim advection (similar to
422        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
423        TAF generates many recomputations) to use it; no yet coded with implicit
424        vertical advection.
425      - change experiment advect_cs (new output) and advect_xy (same output)
426        to test compressible flow multi-dim advection.
427    o pkg/generic_advdiff:
428      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
429        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
430    o pkg/seaice:
431      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
432        bug affects two verification experiments (lab_sea and lab_sea.hb87),
433        recover old (wrong) results by setting noSlipFac = 2. in
434        seaice_calc_strainrates.F;
435      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
436      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
437        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
438      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
439    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
440      - new subroutines seaice_lsr_tridiagu/v
441      - introduce loop bounds i/jmin/max to be able to use a restricted
442        additive Schwarz method, but not used for now.
443      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
444      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
445    o OpenAD support
446       Reorganize S/R call for overall time-stepping loop to facilitate
447       OpenAD revolve loop replacement
448       (new S/R main_do_loop.F)
449    o model/src:
450      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
451      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
452        ADAMS_BASHFORTH2.
453    o pkg/cheapaml:
454      - add new parameter (default=F, same as before) to disable full domain
455        (including land) periodicity in X & Y dir.
456      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
457        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
458        into single S/R CHEAPAML_TIMESTEP.
459    
460    checkpoint64d (2013/02/17)
461    o pkg/monitor (angular momentum):
462      - do not add Eta contribution to the total AM if using rigid-lid;
463      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
464      - horizontal discretisation: compute Zonal wind contribution separately for
465        each component (instead of from cell centered averaged) and use the 4
466        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
467      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
468        FreeSurf) if using vectorInvariant momentum.
469    o model/src (horizontal grid):
470      - move initialisation of all horizontal grid arrays to null value
471        from specific horizontal grid S/R to main S/R INI_GRID;
472      - add 2 new arrays to project model C-grid velocity on to zonal direction
473        (similar to AngleCosC & -AngleSinC but at U and V point location) and
474        compute them in S/R CALC_GRID_ANGLES.
475    o pkg/seaice: replace a hard coded parameter by a runtime parameter
476        SEAICE_JFNK_tolIter
477    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
478        preconditioner for JFNK (run LSR into the overlaps as far as possible,
479        i.e OLx/y-2, but overwrite the solution in the overlaps)
480      - extend loop range in seaice_calc_viscosity
481      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
482      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
483      - slightly modify loops in tridiagonal solver lsr-preconditioner
484      - by default remove the extra exchange in seaice_preconditioner with a
485        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
486      - modify offline_exf_seaice so that old results without RAS are reproduced
487        for output.dyn_jfnk.txt
488      in seaice_fgmres.F (unrelated to RAS)
489      - add a cpp-flag option for a re-ordered mapping (potentially more
490        efficient), but because this changes the results, turn it off by
491        default
492      - replace the save statement by local common blocks
493    o utils/matlab:
494      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
495      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
496        instead of local script "load_cs.m".
497    o pkg/seaice:
498      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
499        to the scalarProductMetric and the unrolling. By chance this does not
500        change the verification experiment, because of the particular domain
501        decomposition
502    o pkg/diagnostics:
503      - change default missing_value from UNSET_RL to -999.
504    o pkg/layers: improve vectorization of layers_fluxcalc.F
505      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
506        time spent in this routine by more than a factor of 3 on an NEC-SX8
507      - step 2: replace search algorithm by a bisection algorithm found in
508        Press et al. Numerical Recipes in Fortran. This algorithm can be
509        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
510        For now, use this algorithm only for TARGET_NEC_SX defined.
511      - moved the search algorithm into a separate subroutine, that is kept
512        within the same file for automatic inlining.
513      - modified catching potential errors
514    o pkg/ecco:
515      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
516    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
517      - modifications for ALLOW_GENTIM2D_CONTROL
518      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
519      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
520      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
521      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
522    o model/src:
523      - account for moist thermodynamics in (dry) potential temperature equation;
524        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
525        and cpl_aim+ocn.
526      - also switch to standard compiler (gfortran, was using ifort previously)
527        for fizhi-cs experiments reference output.
528    o pkg/ctrl:
529      - 1st step toward generic time-varying control variable (2D) via CPP option
530        ALLOW_GENTIM2D_CONTROL
531      - note new namelist ctrl_nml_genarr in data.ctrl
532    o verification/global_ocean.cs32x15:
533      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
534        thsice calling sequence and update "output.icedyn.txt" output file.
535    o pkg/ptracers:
536      - from Ryan A.: code to allow to restart a tracer at regular time interval
537        specifying a reset frequency and a reset-phase (for each tracers).
538    o pkg/thsice:
539      - implement new sequence of calls for thsice+seaice:
540          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
541          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
542      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
543        in CPP_OPTIONS.h) to recover old sequence;
544      - update diagnostics for Intermediate State thsice diagnostics: now filled
545        just before advection (instead of just after advection in old sequence);
546      - update output of experiment offline_exf_seaice (standard test);
547      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
548        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
549    o pkg/aim_v23:
550      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
551      - use standard pkg/mdsio routines to read & write CO2 pickup file;
552      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
553      - Implement new sequence of calls for seaice advection (with thsice and
554        seaice diffusion): do ice advection after ice-Thermodynamic (previously
555        was done before); change aim_do_physics.F (split the bi,bj loops block);
556      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
557    o pkg/thsice:
558      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
559        where just seaice diffusion is used without seaice-dynamics.
560    
561    checkpoint64c (2013/01/18)
562    o pkg/seaice:
563      - add a parameter JFNKres_tFac that can replace JFNKres_t
564        (= JFNKres_tFac*JFNKresidual before JFNK solver)
565      - add a line search option to the JFNK solver
566      - move update of u/vIce and computation of initial residual into a separate
567        routine (same file); makes the code a little easier to read (?)
568      - the line search requires computation of the residual and for some reason
569        I cannot do the update of u/vIce at the beginning of the Newton loop
570        without changing the results, so we move computation of the new residual
571        also to the end of the Newton loop, even without the line search
572    o pkg/mdsio:
573      - write missing value (corresponding to undefined array value) to meta files;
574        skip this if missing value is one (UNSET_RL would be a better value for the
575        case of undefined missing value but it's current the default missing-value);
576        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
577    o pkg/exf & thsice:
578      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
579        diagnostics) even when SHORTWAVE_HEATING is #undef;
580    o verification/cfc_example:
581      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
582        illustrate how to use it).
583    o verification/offline_exf_seaice:
584      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
585        files to only one time-record.
586      in input.thermo: narrow the 2 bands of low initial ice-concentration near
587        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
588        snapshot output; same mcPheePiston value as in thsice with
589        surf-current=0.2m/s.
590      in input.thsice: similar set-up as in input.thermo (channel with same seaice
591        initial conditions).
592    o verification/cfc_example:
593      - update file "data" with more standard choice (default rotationPeriod,
594        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
595        set deltaTFreeSurf to deltaTtracer) and update the output.
596    o pkg/layers:
597      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
598      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
599    o verification/offline_exf_seaice:
600      - set all {field}period to zero for constant-in-time forcing (not tested
601        anywhere else).
602    o verification/offline_exf_seaice:
603      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
604      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
605    o model/src:
606      - implement Finite-Volume method for (hydrostatic) presure gradient
607        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
608    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
609      - In order to be compatible with the default EVP code, this requires changing
610        the EVP code around a little; and because any small change immediately
611        breaks the lab_sea.hb87 verification experiment, the reference output is
612        updated two times (each time the remaining aggrement was only 2 digits):
613        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
614        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
615        The adjoint test lab_sea.evp also needed to be updated.
616      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
617        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
618        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
619        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
620        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
621        kept obscure, because I need to test it a little more.
622    o pkg/cheapaml:
623      - fix few incorrect type (_RL/_RS) in subroutine calls.
624    o pkg/seaice:
625      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
626        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
627    o model/src:
628      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
629        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
630        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
631    o pkg/cheapaml:
632      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
633        update output of experiment cheapAML_box.
634      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
635        and set them only in one place (cheapaml_readparms.F).
636      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
637      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
638        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
639    o model/src/the_main_loop.F:
640      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
641    o pkg/seaice:
642      - remove legacy branch code.
643      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
644    o verification/*/code*/SEAICE_OPTIONS.h:
645      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
646        SEAICE_CAP_HEFF).
647  o pkg/cheapaml:  o pkg/cheapaml:
648    - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time    - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
649      to load new forcing fields.      to load new forcing fields.

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