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revision 1.1784 by jmc, Tue Dec 18 01:22:01 2012 UTC revision 1.1997 by jmc, Mon May 19 14:15:02 2014 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/sbo:
8      - incorporate modifications from Katherine Quinn to enable the use of sbo
9        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
10        output for future testreport verification (unfinished).
11    o pkg/atm_phys:
12      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
13        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
14        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
15    o pkg/seaice
16      seaice_calc_ice_strength.F: modify expression to avoid divisions
17        (affects truncation)
18      seaice_do_ridging.F: clean up the insectarium
19      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
20      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
21      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
22      - add some debugging information and error messages (warnings)
23    o model/src: modifications relatd to atmosphere p*:
24      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
25      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
26        of vertical profile tRef in geopotential background and anomaly.
27      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
28        and pkg/atm_phys.
29      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
30        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
31    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
32    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
33        not used right now, but can be used in BGC packages to fix conservation.
34    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
35        other packages too.
36    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
37        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
38    o model/src:
39      - since we have several heat capacity (even in model/src), define "recip_Cp"
40        as local variable (no longer in common block) to avoid any confusion.
41      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
42    o pkg/exf:
43      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
44        air density as function of air Temp, Humidity and atm pressure.
45    
46    checkpoint64w (2014/05/02)
47    o verification:
48      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
49        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
50        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
51        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
52        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
53    o model/src: for atmosphere in p* coords:
54      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
55      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
56        but not yet activated.
57    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
58      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
59      - this changes the results (but not for any verification experiment, because
60        none tests this), but avoids having an extra field in the restart files
61    o pkg/seaice: remove global variable TICE (not needed)
62      - replace by TICES or local variable where necessary (cost_seaice_test,
63        seaice_diagnostics_state)
64      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
65      - use specific read/write routines for reading and writing individual leves
66        of a multilevel field
67    o pkg/ctrl & model/inc:
68      - move additional anomaly fields of control vars (related to options:
69         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
70        from DYNVARS.h into new header file: CTRL_FIELDS.h
71    o pkg/seaice: some small modifications to the ridging code
72      - make fw2ObyRidge a global variable and add the freshwater flux to
73        seaice_growth
74      - pass actual thickness from seaice_prepare_ridging, so that it is
75        computed only in one place and compute it in the same way as in
76        seaice_growth
77      - initialise more fields in seaice_do_ridging that where cause floating
78        point exceptions over land
79    o pkg/seaice: preparations for ridging code and first real ridging code
80      - move most of "PART 1" of S/R seaice_growth into a new and separate
81        S/R seaice_reg_ridge that will both regularize the state variable after
82        advection call the actual ridging routine;
83      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
84        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
85      - remove ridging code from seaice_advdiff
86      - clean up remaining part 1 of seaice_growth in an attempt to make it
87        more readable (this is probably subjective)
88      - call seaice_itd_redist once in the initialisation phase to have the initial
89        conditions in the correct category
90      - finally: add new ridging routine for ITD code
91    
92    checkpoint64v (2014/04/11)
93    o pkg/ecco:
94      - add runtime parameters mdt[start,end]date[1,2]
95      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
96    o pkg/seaice:
97      - make deltaC a global variable, so that it can be used in ridging code
98      - first step towards ridging: introduce new routines that compute
99        ice strength based on ridging parameters
100      - add diagnostic for HSNOWITD
101      - add opnWtrFrac as a global variable (required for ridging scheme)
102    o pkg/salt_plume + pkg/seaice/seaice_growth.F
103      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
104        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
105    o verification/hs94.1x64x5:
106      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
107      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
108    o autodiff:
109      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
110        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
111        For now, only in pkgs used in verification/hs94.1x64x5.
112      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
113        which are specific to TAF/TAMC).
114      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
115        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
116        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
117      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
118        building mitgcmuv_ad (make adAll).
119    o pkg/ecco:
120      - cost_gencost_seaicev4.F:
121         reformulate proxy cost as function of sst and local param SEAICE_freeze
122         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
123      - add stop statement if old names siv4-[sst,vol] are used
124      - add snapshots + cost reports for atmospheric longwave
125      - remove factor 0.1 in front of wtau[u,v]
126      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
127         ALLOW_TMI_SST_COST_CONTRIBUTION
128    o pkg/atm_phys:
129      - add some diagnostics for Short-wave and for convection S/R.
130    o pkg/seaice/seaice_growth:
131      - fix a bug in the lateral melt parameterization for SEAICE_ITD
132        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
133      - rearrange loop order for better vector code in the same code block
134      - rewrite the floeDiameter formula to have fewer divisions
135      -  (miraculously) none of this changes the results of seaice_itd
136    o pkg/smooth:
137      - move param smooth2Ddiffnbt to pkg/ecco
138    o pkg/salt_plume:
139      - salt_plume_frac.F:
140         clean up local param names
141         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
142    o pkg/rw:
143      - add RS version of S/R READ_MFLDS_LEV.
144    o pkg/streamice:
145      - fix the restart test by writing/reading pickup_streamice files.
146    o pkg/seaice:
147      - refine checks for jfnk-related parameters
148      - comment out if statement with SEAICEuseIMEX parameter as long as there
149        is no IMEX code to avoid confusion and surprises
150    
151    checkpoint64u (2014/03/07)
152    o verification/MLAdjust:
153      - rename secondary test suffix:
154         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
155         0.leithD -> AhFlxF  + switch to flux-form
156         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
157         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
158    o pkg/mom_vecinv:
159      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
160        to be before mom_calc_visc.F)
161      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
162      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
163        this is simpler for the adjoint and for diagnostics.
164    o model/src + pkg/momentum:
165      - add input files for  2-D additional Western and Southern cell-edge wall
166         (e.g., to add "thin-wall" where it is =1).
167      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
168        using 2nd hFacZ that is computed from initial (fix domain) hFac
169      - known limitations of thin wall implementation: not yet coded for sigma
170        coords; not working with CD-scheme neither.
171    o pkg/seaice:
172      - rename recently introduced parameters from (wrong name) AB to
173        BDF (backward difference time discretisation)
174      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
175    o tools/adjoint_options:
176      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
177    
178    checkpoint64t (2014/02/01)
179    o pkg/ecco
180      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
181        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
182      - replace hard-coded record number and period which only work for monthly
183        with read-in runtime param that works for other periods (month,day,year)
184    o pkg/thsice
185      - corrected store directive fixes thsice adjoint gradient checks
186    o genmake2 & testreport:
187      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
188        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
189        Update testreport accordingly. No need to set "export OPENAD=true"
190        in adjoint_options/adjoint_oad anymore (will be removed later).
191    o pkg/shelfice:
192      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
193        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
194        so that surface forcing applies to k=kSurf if using pkg/shelfice.
195    o pkg/ctrl, pkg/grdchk, pkg/ecco:
196      - Changes to make GENARR more modular (i.e. invisible if not used)
197    o model/src/temp_integrate.F and salt_integrate.F
198      - re-include store directives that were removed on Dec 27th.
199    o model/src/external_forcing_surf.F
200      - add storage directives for EmPmR and PmEpR to avoid recomputation of
201        seaice_model in the adjoint that is problematic when seaice_model is
202        turned off in the adjoint. The resolved issue dated back to July when
203        EXTERNAL_FORCING_SURF call was moved.
204        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
205    o pkg/exf/exf_check.F
206      - fix a small bug again (originally found by Wentao Liu, now found again)
207      - streamline error output
208    o pkg/streamice and aim_v23:
209      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
210        Apple's /usr/bin/cpp knows what to do:
211        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
212        Target: x86_64-apple-darwin13.0.0
213    
214    checkpoint64s (2014/01/05)
215    o tools/adjoint_options:
216      - switch to fastopt.net TAF server (instead of default fastopt.de) for
217        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
218    o model/src:
219      - remove some unnecessary TAF storage directives in forward_step.F and
220        in dynamics.F (note: not always removed by TAF, e.g., double storage
221        of kappaRU,kappaRV in former version of dynamics.F).
222    o model/src & pkg/ptracers:
223      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
224        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
225        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
226      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
227      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
228      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
229    o useSingleCpuInput separates single-CPU input from single-CPU output;
230        for now only implemented for in exf_interp_read.F
231    o verification/advect_xy:
232      - fix missing EXCH call in local version of ini_salt.F and update output.
233    o momentum diagnostics:
234      - fix which deltaT is used in Total-Tendency diagnostics.
235      - fix typo in diagnostics for momentum tendency from AB.
236    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
237        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
238    
239    checkpoint64r (2013/12/08)
240    o verification/*/results:
241      - Update reference output of experiments that were passing with just 13 digits
242         (make it easier to detect future changes in results)
243    o model/src & pkg/ptracers:
244      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
245        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
246        to inside ptracers_integrate.F ; remove ptracers_advection.F
247    o coupling interface pkgs:
248        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
249      - change the config check to test the agreement of Ocean Depth
250        with ATM land/sea mask (instead of ATM orography);
251      - send to coupler the number of coupler time-steps to do for this run:
252        this allows to check for consistency and don't need anymore to be
253        specified in parameter file "data";
254      in coupler:
255      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
256      - improve report to log-file of config setting (pass log-file unit to few S/R)
257    o pkg/compon_communic:
258      - add coupling send/receive for non-tiled integer vector;
259      - add S/R to check and stop if any proc has an error (similar to
260        eesupp/src/stop_if_error.F but single thread and across Comm_World).
261    o pkg/exch2:
262      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
263        through list of all tiles my proc owns.
264    o model/src:
265      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
266        from rTrans) to simplify dependencies (no need to store rTrans anymore in
267        calling S/R); this affects AD results at machine truncation level:
268        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
269        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
270    o tools/build_options:
271      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
272    o coupling interface pkgs:
273        [compon_communic, atm_compon_interf & ocn_compon_interf]
274      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
275        to each S/R that needs it; remove un-used variables.
276      - change component tile registration (cpl_register.F in both compon_interf
277        and mitcomponent_tile_register.F) to pass the full list of tiles
278        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
279      - with pkg/exch2: adopt the same convention used for I/O to define mapping
280        towards coupler global array (unless W2_useE2ioLayOut=F):
281         a) can now use different tiling between atm & ocn comp.
282         b) no needs to modify the run-Off map when changing tiling (was needed
283            even if using the same tiling between atm & ocn).
284         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
285            full land tiles); not yet tested.
286      - check for valid mapping from comp. tile to coupler global array
287      - improve report of tile registration results to log file.
288    o pkg/exch2:
289      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
290        tile-registration (CPL_REGISTER);
291      - activate (un-comment) definition and setting of "W2_tileIndex" list to
292        store the local bi,bj indices of each tile;
293      - also print bi,bj in local report to log file;
294      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
295        Jun 2009 modif of pkg/exch2).
296    o testing on baudelaire:
297      - run 2 tests at a time: no significant slow down (since enough cpu) and
298        get the full set of test done earlier
299      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
300    o model/src/thermodynamics.F and routines called from it:
301      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
302        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
303        velocity (outp) by adding bolus velocity.
304      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
305        mass transport from velocity + lateral grid cell area
306      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
307      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
308     in thermodynamics.F
309      - remove k from thermodynamics.F and move it to temp_integrate.F
310        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
311        loop).
312      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
313        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
314        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
315        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
316      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
317        global_ocean.90x40x15, tutorial_global_oce_biogeo and
318        tutorial_tracer_adjsens (+ TLM output).
319    o tools/OAD_support and (verification/*/) code_oad:
320      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
321        module conversion ; remove unneeded CPP_EEOPTIONS.h.
322      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
323        version (closer to model/inc/CPP_OPTIONS.h).
324    o model/src:
325      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
326        retired list of parameters (routine FREEZE has been replace by surface
327        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
328    o pkg/gmredi:
329      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
330        velocity (same scheme but affects machine truncation) for GM_AdvForm.
331      - update output of FWD experiments: front_relax.bvp,
332        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
333    
334    checkpoint64q (2013/11/17)
335    o verification:
336      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
337        tutorial_global_oce_biogeo and global_ocean.90x40x15.
338      - generate new output (growth & melt) for seaice_itd experiment after
339        updating the input pickup_seaice files (previously wrong).
340    o pkg/cost:
341      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
342        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
343        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
344          cannot be applied to var in common block).
345        o allows to get results independent of tile-per-proc setting (if using
346          slower GLOBAL_SUM_SEND_RECV option).
347      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
348        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
349        forward gradients: update output).
350      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
351        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
352    o pkg/mom_common:
353      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
354        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
355        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
356        ensure that all field value that are used are set.
357    o tutorial_deep_convection (smag3d):
358      - add missing scaling in mom_calc_smag_3d.F;
359      - set smag3D_coeff in input.smag3d such that results do not change.
360    o pkg/dic:
361      - change dic_cost.F to compute cost on each tile first and then apply
362        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
363        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
364      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
365    o eesupp/src & pkg/mdsio:
366      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
367        (from pkg/mdsio) since they are no longer used for tape IO.
368      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
369        (+ keep a copy in pkg/atm_ocn_coupler).
370    o verification/isomip:
371      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
372    o tools/build_options:
373      - optfile linux_amd64_ifort11, fast (no ieee) case:
374        to get a working restart for all experiments, add "-fp-model source"
375        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
376    
377    checkpoint64p (2013/10/20)
378    o pkg/autodiff:
379      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
380        criteria, return to simple (default) tape IO format.
381    o pkg/mdsio (+ eesupp/src):
382      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
383        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
384      - fix globalFile and singleCpuIO options using simpler global mapping.
385      - new pairs of scatter/gather vector S/R (one for each type, generated from
386        template) corresponding to simpler global mapping.
387      - adread_write.F: switch to new S/R (but leave old calls commented) and write
388        to globalFile when parameter globalFiles is set to True.
389      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
390    o pkg/autodiff:
391      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
392        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
393        missing, just add a STOP if array type do not match.
394    o pkg/exf:
395      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
396         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
397         and rename array obsSIce to exf_iceFraction.
398    o tutorial_deep_convection:
399      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
400        for now all in this exp. code dir.
401      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
402        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
403    o eesupp/src:
404      - added SINGLE_DISK_IO option because reading of parameter files on
405        very large number of processors did not work with existing set-up
406    
407    checkpoint64o (2013/09/25)
408    o pkg/atm_phys & atm_compon_interf:
409      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
410    o tools/build_options:
411      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
412        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
413        remove CPP setting (was identical to genmake2 default).
414    o pkg/gmredi & model/src: Some updating and work done on the residual model.
415      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
416      - fixed up the calculation of the eddy stress and how it is added to the
417        external forcing via taueddy_external_forcing.F
418      - at the moment, it is very experimental and only works with the variable eddy
419        diffusivity calculated in gmredi_k3d.F
420    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
421        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
422    o testreport (& tools/do_tst_2+2):
423      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
424    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
425      - remove CPP='cpp -traditional -P' (this is genmake2 default)
426      - add switch (for big setups) to use 'medium' memory-model (but leave it
427        commented out for now). Note: needed with FC 19 to compile big setups.
428    o pkg/atm_compon_interf:
429      - regroup per field origin (model & pkgs) the coupling storage routines
430         (which accumalate in time each coupling field)
431      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
432        update accordingly + simplify aim_do_physics.F
433    
434    checkpoint64n (2013/08/26)
435    o pkg/bbl:
436      - update formulation to reduce dispersion of tracer properties in bbl
437      - replaced horizontal and vertical transport parameters with velocities
438      - changes results for verification/global_with_exf.yearly
439    o verification/halfpipe_streamice:
440      - change to matrix construction; update both Fwd & AD output.
441    o verification/tutorial_tracer_adjsens:
442      - OpenAD test: switch to vector-invariant momentum since fluxform with
443        rStar causes problems with OpenAD; update output.
444    o tools:
445      - genmake2: define a common prefix for all temp-file names ; move them
446        to local /tmp disk (but would be easy to move them back);
447      - xmakedepend: apply the same switch for temp-files.
448    o pkg/offline:
449      - changes for use with rStar (NLFS): assume that we continue to provide
450        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
451        output files) and apply r* scaling at each time-step (function of the time
452        varying Eta field); use normal pickup files (needed for restart with NLFS).
453    o adjoint with OpenAD:
454      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
455        package openad.  This package has to be compiled for all runs with OpenAD
456        instead of specifying code_oad_all as a modification directory.
457      - link the fortran templates from tools/OAD_support to the build directory
458        for preprocessing to avoid conflicts between different setups compiled
459        simultaneously and simplify cleanup.
460    o pkg/exf:
461      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
462        main model or other pkgs are exchanged in EXF_MAPFIELDS).
463    o model/src:
464      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
465        (similar to do_fields_blocking_exchanges.F).
466    o tools/genmake2:
467      - remove TAF output src code just before calling staf (when not doing a fresh
468        built, will stop if things go wrong with staf).
469      - fix target "adobj" (left from TAF version-2 transition)
470    o pkg/diagnostics:
471      - add a parameter to track the status of pkg/diagnostics activation;
472        this replace/extend the use of logical param "settingDiags" (to check
473        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
474        New S/R to print error message and stop when pkgStatus is not right.
475      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
476    
477    checkpoint64m (2013/08/13)
478    o model/inc:
479      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
480        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
481    o pkg/kpp & aim_v23:
482      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
483    o pkg/seaice:
484      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
485        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
486      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
487    o eesupp/src:
488      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
489        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
490    o switch to TAF version-2:
491      - add flow directives to "freeze" naming convention for ad-routines that
492        are used in I/O routines of adjoint state and associated common blocks
493        that are used in adcommon.h (backward compatible with version-1)
494      - update all ad-optfiles (in tools/adjoint_options + few local to some
495        verification exp) to switch to latest TAF version (currently 2.5.5);
496        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
497        out except for diva).
498      - the major change with TAF version-2 is that both the differentiated
499        routines and the forward routines (new) are returned as part of the TAF
500        output source code. Update genmake2 accordingly.
501      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
502        with version-2 when compared to TLM or FWD gradient); other experiments
503        output show minor changes (machine truncation level); update the few AD &
504        TLM output with 12 matching digits only (some prior to version-2 switch).
505    
506    checkpoint64l (2013/08/05)
507    o model/src:
508      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
509      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
510        when using TAF but only if using OpenAD.
511    o pkg/mom_common+fluxform+vecinv:
512      - always set horiz. viscosity arrays to background value before calling
513        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
514        only when using variable horiz. viscosity (useVariableVisc=T);
515      - simplify mom_vecinv.F (only 1 block for momViscosity).
516    o pkg/mom_common: variable horiz. viscosity in NH code
517      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
518        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
519      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
520        useBiharmonicVisc & useVariableVisc.
521      - fix old bug (already in 1rst implementation of variable horizontal viscosity
522        in calc_gw.F, version 1.27, 2006/06/20):
523        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
524        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
525      - change background horiz viscosity in vertical momentum (gW) to always be
526        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
527        any type of variable viscosity, e.g., viscAh/4Grid)
528      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
529        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
530        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
531        default viscAh,viscA4 is zero).
532    o model/src:
533      - extend length of drC & recip_drC from Nr to Nr+1.
534    o Divided Adjoint (DIVA) with MPI:
535      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
536      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
537        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
538    
539    checkpoint64k (2013/07/23)
540    o tools/OAD_support:
541      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
542        and remove it from genmake2.
543    o tools/build_options:
544      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
545        MPI_HEADER_FILES list (let genmake2 find the missing headers)
546    o verification/halfpipe_streamice:
547      - change to driving stress formulation; update both Fwd & AD output.
548    o tools/genmake2 and Divided Adjoint with MPI:
549      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
550      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
551      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
552        Makefile, which is set by genmake2, and check which mpi-headers are needed.
553        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
554      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
555    o testreport:
556      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
557        perform additional runs (number of additional runs is "add_DIVA_runs" taken
558        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
559    o verification/lab_sea (AD test):
560      - change to test Divided Adjoint Run in this set-up (both standard AD test
561        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
562    o pkg atm_ & ocn_compon_interf:
563      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
564        staggerTimeStep implementation) and disable (retired) corresponding
565        parameter.
566    o pkg/offline:
567      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
568      - add S/R OFFLINE_CHECK to print offline parameter summary
569        and stop if loading a file that is not used;
570      - enable to calculate GMRedi tensor, KPP mixing and convective index
571        when the corresponding file(s) is/are not specified (but pkg is used).
572      - comment out resetting of monitorFreq (to endTime) since it still useful
573        for monitoring CFL numbers and checking offline fields.
574    o OpenAD:
575      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
576        smaller standard output) and generate new (smaller) output (on baudelaire
577        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
578    o model/src:
579      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
580        (where external_forcing_adjust was called) and change list of arguments;
581      - merge external_forcing_adjust.F into external_forcing_surf.F
582      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
583        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
584        previously in file "balance_relax.F", now removed); remove corresponding
585        arrays in FFIELDS.h.
586      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
587        a hack for getting back surfaceForcingS (loaded from file) when using
588        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
589      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
590        (was getting only 11 digits for AD-grad, due to different truncation
591         error in AD code).
592    
593    checkpoint64j (2013/07/04)
594    o pkg/offline:
595      - to enable the use of other features with pkg offline (e.g., obcs),
596        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
597      - comment out "allowFreezing" (now active) in 2 offline testing exp.
598    o pkg/exf ALLOW_RUNOFTEMP
599      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
600      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
601      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
602    o pkg/atm_phys:
603      - allows to add some damping on uVel,vVel (strength only function of k).
604    o verification, ad-tests:
605      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
606        global_ocean_ebm and offline_exf_seaice.thsice.
607    o verification/halfpipe_streamice:
608      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
609        flux input boundary conditions to be ignored; a fix for this bug changed
610        verification results for forward test.
611      - add adjoint test.
612    o pkg/ptracers:
613      - allow to restart without SOM pickup (resetting SOM to zero).
614    o pkg/gmredi:
615      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
616      - It uses mixing length theory and suppression by steering level effects to
617        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
618        to JPO, for more details).
619      - It also uses the diffusivity to calculate an eddy induced streamfunction
620        based on a PV closure (rather than a buoyancy closure as in GM).
621      - New files added to pkg/gmredi:
622        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
623          induced overturning streamfunction (called from gmredi_calc_tensor)
624        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
625          for use in gmredi_k3d
626        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
627          the eddy diffusivity
628    
629    checkpoint64i (2013/06/18)
630    o pkg/cheapaml:
631      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
632        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
633        with pkg/cheapaml.
634    o utils/python: add subpackage for cubed sphere function, first example is
635        simple cs.pcol to plot 2D fields on a map
636    o pkg/streamice:
637      - This is a new package in MITgcm, which solves dynamic equations for ice
638         sheets and ice streams
639      - At the moment it is independent of atmosphere/ocean dynamics, or any
640        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
641        ed that this will change)
642      - There is a new verification exercise that tests it, halfpipe_streamice,
643        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
644        rectangular embayment
645      - halfpipe_streamice is forward-only for now, will have TAF test soon
646      - for questions, email dgoldber@mit.edu
647    o pkg/thsice:
648      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
649        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
650      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
651         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
652      - allow precip from pkg/cheapaml to make snow over seaice.
653    o pkg/cfc:
654      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
655      - remove atmos CFC 2-D arrays from common bloc (now local variables)
656      - change some hard-coded constant to run time parameter for reading and
657        and interpolating atmospheric CFC ; keep same default as previously.
658      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
659      - put arguments in standard order: myTime, myIter, myThid
660      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
661        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
662      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
663      - new routine to print summary of CFC params and check for consistency.
664    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
665      similar to thsice_advdiff.
666      Note that for the B-grid case the routine parameters uc/vc are overwritten.
667    o pkg/cfc:
668      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
669        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
670      - fix interpolation of atmphspheric CFC between Sorthern and Northern
671        hemisphere value.
672    o pkg/seaice:
673      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
674    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
675                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
676      - requires an additional time level that is stored in the pickup
677      - you can start with AB2 from a pickup without this time level with
678        pickupStrictlyMatch = .false.
679    
680    checkpoint64h (2013/05/26)
681    o pkg/cheapaml:
682      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
683        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
684      - consistent treatment of uWind,vWind location: assume everywhere in
685        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
686        (Note: was already the case for Tair,Qair advection);
687        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
688      - compute diabatic forcing only in the interior (excluding overlap regions)
689      - fill in array "Qsw" (for short-wave heating);
690      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
691        before any update (consistent with MITgcm state var diagnostics);
692      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
693        non periodic ; + adjusted for uWind,vWind (C-grid).
694    o pkg/seaice:
695      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
696        add explicitly pkg/exf in experiments that currently use pkg/seaice.
697      - allows to compile pkg/seaice without pkg/exf.
698    o tools/OAD_support:
699      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
700        of array "ourStepOf" in function rvNextAction (revolve.F90).
701    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
702      - change pkg name (to be used with other atmospheric physics pkg)
703        but by-pass CVS when making the new pkg so that we keep the CVS history.
704    o pkg/offline:
705      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
706        (previously called from pkg/dic_surfforcing_init.F)
707    o model/src:
708      - re-order sequence of calls within packages_init_variables.F, using
709        standard order, except for:
710         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
711         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
712    o new pkg: atm_phys
713      - add entry point and source code (previously in contrib
714          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
715        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
716      - re-order sequence of calls within packages_readparms.F,
717         packages_init_fixed.F and packages_write_pickup.F
718        (but skip packages_init_variables.F because of TAF issues).
719      - update contrib/*/atm_gray/ experiment.
720    o pkg/seaice (ITD code):
721      - simplify and fix the writing of pickup-files for ITD case
722    o pkg/seaice (ITD code):
723      - introduce floe size dependent lateral melt for ITD case;
724      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
725      - update seaice_itd experiment main output.
726    o pkg/thsice:
727      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
728        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
729        changed accordingly pkg/atm2d.
730    
731    checkpoint64g (2013/05/01)
732    o pkg/exf ALLOW_RUNOFTEMP
733      - if defined,  river and glacier runoff temperature can be read-in from
734        runoftempfile; runoftempfile needs to have same format as runofffile
735    o pkg/thsice (& pkg/bulk_force):
736      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
737        for energy content of Precip + RunOff & Evap (like with pkg/exf).
738      - change computation domain to always be the interior (without overlap).
739      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
740    o verification/tutorial_global_oce_biogeo:
741      - add preliminary OpenAD setup (still has problems)
742    o pkg/seaice:
743      - turn some parameters for choosing the convergence criterion of
744        the inexact Newton method (JFNK) into runtime parameters for convenience
745      - clean up seaice_calc_viscosities.F: remove/retire two options for
746        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
747        the results of lab_sea/input because a division has been replaced by
748        a multiplication with the reciprocal (sumNorm)
749      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
750        convergence of solver (changes results, of course), and to test some
751        new features
752    o model/src:
753      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
754      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
755      - move forcing adjustment (balancing surface forcing) in specific S/R
756        where might also be applied exchanges (if needed) to forcing arrays.
757    o pkg/shelfice:
758      - allow to specify the Ice-Shelf mass per unit area (instead of
759        shelficeLoadAnomaly) and do the conversion from one to the other
760      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
761        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
762        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
763        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
764      - update isomip experiment forward output (get machine truncation error
765        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
766    o verification/offline_exf_seaice:
767      revise data.seaice in input.thermo and input_ad and update results accordingly
768        HO = 0.2, SEAICE_areaLossFormula = 2,
769        SEAICE_growMeltByConv = .TRUE.,
770        SEAICE_doOpenWaterMelt = .TRUE.,
771      Improve consistency with input.thsice and fix the spurious 500m ice corners
772    o verification/global_ocean.cs32x15:
773      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
774        in icedyn (thsice+seaice-dyn) test and update output.
775    o verification/offline_exf_seaice:
776      - adjust list of tested variables (with testreport) and update
777        standard test output with better slection of monitored fields.
778    o pkg/cd_code:
779      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
780        experiment lab_sea.hb87
781    o tools/genmake2:
782      - change default makedepend from the system default to tools/xmakedepend:
783        When no makedepend is specified, select tools/xmakedepend it the test pass,
784        otherwise select the system default (if exist and pass the test) or
785        try to build cyrus-makedepend ; stop if none of the 3 works.
786    o pkg/exf & pkg/thsice:
787      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
788        for energy content of Precip + RunOff & Evap. Assumes:
789       1) Rain has same temp as Air.
790       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
791       3) Run-Off comes at the temp of surface water (with same Cp)
792       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
793        put directly into Latent Heat flux & should use water-vapor heat capacity.
794       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
795        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
796    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
797        (compile when SEAICE_ALLOW_JFNK is defined)
798    o pkg/thsice:
799      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
800        implementation): move THSICE_AVE call after the advection (called directly
801        from thsice_do_advect.F).
802    o verification/global_ocean.90x40x15 and OpenAD:
803      New experiment for OpenAD is identical to the one in input_ad except that
804        multiDimAdvection=.FALSE.,
805      There is still an issue with this.
806    o pkg/thsice:
807      - account for ice velocity (ocean relative velocity) in turbulent heat flux
808        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
809        and offline_exf_seaice (main test).
810    
811    checkpoint64f (2013/03/31)
812    o verification/OpenAD:
813      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
814    o verification/isomip, pkg/shelfice and OpenAD:
815      - add OpenAD setup to this exp and make shelfice package work with OpenAD
816    o verification/tutorial_global_oce_biogeo:
817      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
818    o verification/offline_exf_seaice:
819      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
820    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
821      - add OpenAD setup to this exp and make ptracers package work with OpenAD
822    o pkg/seaice/seaice_evp.F:
823       mask the asymmetric contribution of the ice-ocean stress (when
824       the turningAngle is non-zero) over open water to avoid stripes
825       in the EVP-solutions after many EVP-substeps. This does not change
826       the verification experiment (because turningAngle=0 in that experiment),
827       but will affect other EVP solutions with turningAngle.ne.0
828    o verification, AD & TLM output:
829      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
830        additions and multiplications which affect results at machine truncation
831        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
832        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
833        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
834        digits of matching.
835    o pkg/seaice:
836       modify lsr-algorithm so that it vectorizes AND converges by using a
837       "zebra" method: split vector loop into two with step size 2; this
838       solves a general convergence problem for the JFNK solver on a vector
839       computer. It has the potential to even improve convergence for
840       non-vector machines, but it does change the results so it is turned
841       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
842       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
843    
844    checkpoint64e (2013/03/05)
845    o pkg/ecco and several verification experiments:
846       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
847       from ecco package, and revert to unified routine in model/src/
848       Adjust verification experiments accordingly, especially gloal_oce_llc90
849       Should conclude long-standing work by Gael to reconsile the_main_loop with
850       ECCO and will enable OpenAD's revolve loop in ECCO setup.
851    o pkg/generic_advdiff:
852      - implement compressible flow method for multi-dim advection (similar to
853        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
854        TAF generates many recomputations) to use it; no yet coded with implicit
855        vertical advection.
856      - change experiment advect_cs (new output) and advect_xy (same output)
857        to test compressible flow multi-dim advection.
858    o pkg/generic_advdiff:
859      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
860        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
861    o pkg/seaice:
862      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
863        bug affects two verification experiments (lab_sea and lab_sea.hb87),
864        recover old (wrong) results by setting noSlipFac = 2. in
865        seaice_calc_strainrates.F;
866      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
867      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
868        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
869      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
870    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
871      - new subroutines seaice_lsr_tridiagu/v
872      - introduce loop bounds i/jmin/max to be able to use a restricted
873        additive Schwarz method, but not used for now.
874      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
875      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
876    o OpenAD support
877       Reorganize S/R call for overall time-stepping loop to facilitate
878       OpenAD revolve loop replacement
879       (new S/R main_do_loop.F)
880    o model/src:
881      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
882      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
883        ADAMS_BASHFORTH2.
884    o pkg/cheapaml:
885      - add new parameter (default=F, same as before) to disable full domain
886        (including land) periodicity in X & Y dir.
887      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
888        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
889        into single S/R CHEAPAML_TIMESTEP.
890    
891    checkpoint64d (2013/02/17)
892    o pkg/monitor (angular momentum):
893      - do not add Eta contribution to the total AM if using rigid-lid;
894      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
895      - horizontal discretisation: compute Zonal wind contribution separately for
896        each component (instead of from cell centered averaged) and use the 4
897        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
898      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
899        FreeSurf) if using vectorInvariant momentum.
900    o model/src (horizontal grid):
901      - move initialisation of all horizontal grid arrays to null value
902        from specific horizontal grid S/R to main S/R INI_GRID;
903      - add 2 new arrays to project model C-grid velocity on to zonal direction
904        (similar to AngleCosC & -AngleSinC but at U and V point location) and
905        compute them in S/R CALC_GRID_ANGLES.
906    o pkg/seaice: replace a hard coded parameter by a runtime parameter
907        SEAICE_JFNK_tolIter
908    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
909        preconditioner for JFNK (run LSR into the overlaps as far as possible,
910        i.e OLx/y-2, but overwrite the solution in the overlaps)
911      - extend loop range in seaice_calc_viscosity
912      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
913      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
914      - slightly modify loops in tridiagonal solver lsr-preconditioner
915      - by default remove the extra exchange in seaice_preconditioner with a
916        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
917      - modify offline_exf_seaice so that old results without RAS are reproduced
918        for output.dyn_jfnk.txt
919      in seaice_fgmres.F (unrelated to RAS)
920      - add a cpp-flag option for a re-ordered mapping (potentially more
921        efficient), but because this changes the results, turn it off by
922        default
923      - replace the save statement by local common blocks
924    o utils/matlab:
925      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
926      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
927        instead of local script "load_cs.m".
928    o pkg/seaice:
929      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
930        to the scalarProductMetric and the unrolling. By chance this does not
931        change the verification experiment, because of the particular domain
932        decomposition
933    o pkg/diagnostics:
934      - change default missing_value from UNSET_RL to -999.
935    o pkg/layers: improve vectorization of layers_fluxcalc.F
936      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
937        time spent in this routine by more than a factor of 3 on an NEC-SX8
938      - step 2: replace search algorithm by a bisection algorithm found in
939        Press et al. Numerical Recipes in Fortran. This algorithm can be
940        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
941        For now, use this algorithm only for TARGET_NEC_SX defined.
942      - moved the search algorithm into a separate subroutine, that is kept
943        within the same file for automatic inlining.
944      - modified catching potential errors
945    o pkg/ecco:
946      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
947    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
948      - modifications for ALLOW_GENTIM2D_CONTROL
949      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
950      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
951      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
952      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
953    o model/src:
954      - account for moist thermodynamics in (dry) potential temperature equation;
955        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
956        and cpl_aim+ocn.
957      - also switch to standard compiler (gfortran, was using ifort previously)
958        for fizhi-cs experiments reference output.
959    o pkg/ctrl:
960      - 1st step toward generic time-varying control variable (2D) via CPP option
961        ALLOW_GENTIM2D_CONTROL
962      - note new namelist ctrl_nml_genarr in data.ctrl
963    o verification/global_ocean.cs32x15:
964      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
965        thsice calling sequence and update "output.icedyn.txt" output file.
966    o pkg/ptracers:
967      - from Ryan A.: code to allow to restart a tracer at regular time interval
968        specifying a reset frequency and a reset-phase (for each tracers).
969    o pkg/thsice:
970      - implement new sequence of calls for thsice+seaice:
971          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
972          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
973      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
974        in CPP_OPTIONS.h) to recover old sequence;
975      - update diagnostics for Intermediate State thsice diagnostics: now filled
976        just before advection (instead of just after advection in old sequence);
977      - update output of experiment offline_exf_seaice (standard test);
978      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
979        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
980    o pkg/aim_v23:
981      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
982      - use standard pkg/mdsio routines to read & write CO2 pickup file;
983      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
984      - Implement new sequence of calls for seaice advection (with thsice and
985        seaice diffusion): do ice advection after ice-Thermodynamic (previously
986        was done before); change aim_do_physics.F (split the bi,bj loops block);
987      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
988    o pkg/thsice:
989      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
990        where just seaice diffusion is used without seaice-dynamics.
991    
992    checkpoint64c (2013/01/18)
993    o pkg/seaice:
994      - add a parameter JFNKres_tFac that can replace JFNKres_t
995        (= JFNKres_tFac*JFNKresidual before JFNK solver)
996      - add a line search option to the JFNK solver
997      - move update of u/vIce and computation of initial residual into a separate
998        routine (same file); makes the code a little easier to read (?)
999      - the line search requires computation of the residual and for some reason
1000        I cannot do the update of u/vIce at the beginning of the Newton loop
1001        without changing the results, so we move computation of the new residual
1002        also to the end of the Newton loop, even without the line search
1003    o pkg/mdsio:
1004      - write missing value (corresponding to undefined array value) to meta files;
1005        skip this if missing value is one (UNSET_RL would be a better value for the
1006        case of undefined missing value but it's current the default missing-value);
1007        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
1008    o pkg/exf & thsice:
1009      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
1010        diagnostics) even when SHORTWAVE_HEATING is #undef;
1011    o verification/cfc_example:
1012      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
1013        illustrate how to use it).
1014    o verification/offline_exf_seaice:
1015      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
1016        files to only one time-record.
1017      in input.thermo: narrow the 2 bands of low initial ice-concentration near
1018        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
1019        snapshot output; same mcPheePiston value as in thsice with
1020        surf-current=0.2m/s.
1021      in input.thsice: similar set-up as in input.thermo (channel with same seaice
1022        initial conditions).
1023    o verification/cfc_example:
1024      - update file "data" with more standard choice (default rotationPeriod,
1025        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
1026        set deltaTFreeSurf to deltaTtracer) and update the output.
1027    o pkg/layers:
1028      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
1029      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
1030    o verification/offline_exf_seaice:
1031      - set all {field}period to zero for constant-in-time forcing (not tested
1032        anywhere else).
1033    o verification/offline_exf_seaice:
1034      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
1035      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
1036    o model/src:
1037      - implement Finite-Volume method for (hydrostatic) presure gradient
1038        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
1039    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
1040      - In order to be compatible with the default EVP code, this requires changing
1041        the EVP code around a little; and because any small change immediately
1042        breaks the lab_sea.hb87 verification experiment, the reference output is
1043        updated two times (each time the remaining aggrement was only 2 digits):
1044        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
1045        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
1046        The adjoint test lab_sea.evp also needed to be updated.
1047      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
1048        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
1049        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
1050        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
1051        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
1052        kept obscure, because I need to test it a little more.
1053    o pkg/cheapaml:
1054      - fix few incorrect type (_RL/_RS) in subroutine calls.
1055    o pkg/seaice:
1056      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
1057        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
1058    o model/src:
1059      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
1060        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
1061        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
1062    o pkg/cheapaml:
1063      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
1064        update output of experiment cheapAML_box.
1065      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
1066        and set them only in one place (cheapaml_readparms.F).
1067      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
1068      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
1069        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
1070    o model/src/the_main_loop.F:
1071      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
1072    o pkg/seaice:
1073      - remove legacy branch code.
1074      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
1075    o verification/*/code*/SEAICE_OPTIONS.h:
1076      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
1077        SEAICE_CAP_HEFF).
1078    o pkg/cheapaml:
1079      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
1080        to load new forcing fields.
1081      - add missing "_d 0" where it's needed; + some editing (improve indentation).
1082      - remove switch to "-r8" compiler option (no longer needed) in verification
1083        cheapAML_box, keep same output (small trucation error differences).
1084    o verification/offline_exf_seaice:
1085      - add thermodynamics only test.
1086    o verification/cheapAML_box:
1087      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
1088        keep same output (same 14 digits for cg2d).
1089      - switch on "-r8" compiler option (some numerical values are missing
1090        the "_d 0") and update output (only 6 digits for cg2d were preserved).
1091    
1092    checkpoint64b (2012/12/24)
1093    o pkg/cheapaml:
1094      - remove un-used variables (Qnet,EmPmR) from pickup files.
1095      - store tendency of advected variables into cheapaml pickup file
1096        and fix the AB-2 restart.
1097    o verification/offline_exf_seaice and lab_sea adjoint:
1098      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
1099      - switch to 4 time steps in offline, consistent with lab_sea.
1100      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
1101      - update results after change of experiment seaice.
1102    o pkg/seaice:
1103      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
1104        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
1105        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
1106        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
1107    o model/src:
1108      - add run-time parameter to select CG2D solver minimum-residual solution
1109        (in case of a poor convergence).
1110    o pkg/seaice/seaice_lsr.F
1111      - move calculation of matrix coefficients into new
1112        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
1113        file; the main purpose of this change is to be able to reuse the code
1114        in S/R SEAICE_PRECONDITIONER
1115      - modify the computation of the residual so that the mass of sea-ice
1116        is not used twice; this simplifies the calculations, but since
1117        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
1118        not tested in testreport---this does not affect the testreport results.
1119    o verification/seaice_obcs:
1120      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
1121        verification/lab_sea/input.salt_plume; changes results/output.txt*
1122  o model/src:  o model/src:
1123    - adapt quasi-hydrostatic formulation to work with p or p* coordinate.    - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
1124  o pkg/seaice:  o pkg/seaice:
# Line 32  o pkg/seaice: Line 1147  o pkg/seaice:
1147    - add a verification experiment for JFNK in offline_exf_seaice    - add a verification experiment for JFNK in offline_exf_seaice
1148  o verification:  o verification:
1149    - change (for now, only fwd test) offline_exf_seaice experiment:    - change (for now, only fwd test) offline_exf_seaice experiment:
1150      use a re-entrant channel with idealized costline (trapezoidal shape)      use a re-entrant channel with idealized coastline (trapezoidal shape)
1151      at southern boundary to explore seaice dynamics and thermodynamics      at southern boundary to explore seaice dynamics and thermodynamics
1152      with simple forcing. Main set-up has dynamics+thermo and SST relaxation;      with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
1153      secondary test (input.thsice) use thermodynamics only with SST relaxation.      secondary test (input.thsice) use thermodynamics only with SST relaxation.
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