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revision 1.1881 by m_bates, Tue Jun 18 21:30:33 2013 UTC revision 1.1993 by jmc, Mon May 12 03:37:11 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 model/src: modifications relatd to atmosphere p*:
8      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
9      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
10        of vertical profile tRef in geopotential background and anomaly.
11      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
12        and pkg/atm_phys.
13      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
14        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
15    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
16    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
17        not used right now, but can be used in BGC packages to fix conservation.
18    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
19        other packages too.
20    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
21        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
22    o model/src:
23      - since we have several heat capacity (even in model/src), define "recip_Cp"
24        as local variable (no longer in common block) to avoid any confusion.
25      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
26    o pkg/exf:
27      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
28        air density as function of air Temp, Humidity and atm pressure.
29    
30    checkpoint64w (2014/05/02)
31    o verification:
32      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
33        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
34        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
35        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
36        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
37    o model/src: for atmosphere in p* coords:
38      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
39      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
40        but not yet activated.
41    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
42      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
43      - this changes the results (but not for any verification experiment, because
44        none tests this), but avoids having an extra field in the restart files
45    o pkg/seaice: remove global variable TICE (not needed)
46      - replace by TICES or local variable where necessary (cost_seaice_test,
47        seaice_diagnostics_state)
48      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
49      - use specific read/write routines for reading and writing individual leves
50        of a multilevel field
51    o pkg/ctrl & model/inc:
52      - move additional anomaly fields of control vars (related to options:
53         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
54        from DYNVARS.h into new header file: CTRL_FIELDS.h
55    o pkg/seaice: some small modifications to the ridging code
56      - make fw2ObyRidge a global variable and add the freshwater flux to
57        seaice_growth
58      - pass actual thickness from seaice_prepare_ridging, so that it is
59        computed only in one place and compute it in the same way as in
60        seaice_growth
61      - initialise more fields in seaice_do_ridging that where cause floating
62        point exceptions over land
63    o pkg/seaice: preparations for ridging code and first real ridging code
64      - move most of "PART 1" of S/R seaice_growth into a new and separate
65        S/R seaice_reg_ridge that will both regularize the state variable after
66        advection call the actual ridging routine;
67      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
68        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
69      - remove ridging code from seaice_advdiff
70      - clean up remaining part 1 of seaice_growth in an attempt to make it
71        more readable (this is probably subjective)
72      - call seaice_itd_redist once in the initialisation phase to have the initial
73        conditions in the correct category
74      - finally: add new ridging routine for ITD code
75    
76    checkpoint64v (2014/04/11)
77    o pkg/ecco:
78      - add runtime parameters mdt[start,end]date[1,2]
79      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
80    o pkg/seaice:
81      - make deltaC a global variable, so that it can be used in ridging code
82      - first step towards ridging: introduce new routines that compute
83        ice strength based on ridging parameters
84      - add diagnostic for HSNOWITD
85      - add opnWtrFrac as a global variable (required for ridging scheme)
86    o pkg/salt_plume + pkg/seaice/seaice_growth.F
87      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
88        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
89    o verification/hs94.1x64x5:
90      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
91      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
92    o autodiff:
93      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
94        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
95        For now, only in pkgs used in verification/hs94.1x64x5.
96      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
97        which are specific to TAF/TAMC).
98      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
99        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
100        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
101      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
102        building mitgcmuv_ad (make adAll).
103    o pkg/ecco:
104      - cost_gencost_seaicev4.F:
105         reformulate proxy cost as function of sst and local param SEAICE_freeze
106         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
107      - add stop statement if old names siv4-[sst,vol] are used
108      - add snapshots + cost reports for atmospheric longwave
109      - remove factor 0.1 in front of wtau[u,v]
110      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
111         ALLOW_TMI_SST_COST_CONTRIBUTION
112    o pkg/atm_phys:
113      - add some diagnostics for Short-wave and for convection S/R.
114    o pkg/seaice/seaice_growth:
115      - fix a bug in the lateral melt parameterization for SEAICE_ITD
116        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
117      - rearrange loop order for better vector code in the same code block
118      - rewrite the floeDiameter formula to have fewer divisions
119      -  (miraculously) none of this changes the results of seaice_itd
120    o pkg/smooth:
121      - move param smooth2Ddiffnbt to pkg/ecco
122    o pkg/salt_plume:
123      - salt_plume_frac.F:
124         clean up local param names
125         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
126    o pkg/rw:
127      - add RS version of S/R READ_MFLDS_LEV.
128    o pkg/streamice:
129      - fix the restart test by writing/reading pickup_streamice files.
130    o pkg/seaice:
131      - refine checks for jfnk-related parameters
132      - comment out if statement with SEAICEuseIMEX parameter as long as there
133        is no IMEX code to avoid confusion and surprises
134    
135    checkpoint64u (2014/03/07)
136    o verification/MLAdjust:
137      - rename secondary test suffix:
138         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
139         0.leithD -> AhFlxF  + switch to flux-form
140         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
141         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
142    o pkg/mom_vecinv:
143      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
144        to be before mom_calc_visc.F)
145      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
146      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
147        this is simpler for the adjoint and for diagnostics.
148    o model/src + pkg/momentum:
149      - add input files for  2-D additional Western and Southern cell-edge wall
150         (e.g., to add "thin-wall" where it is =1).
151      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
152        using 2nd hFacZ that is computed from initial (fix domain) hFac
153      - known limitations of thin wall implementation: not yet coded for sigma
154        coords; not working with CD-scheme neither.
155    o pkg/seaice:
156      - rename recently introduced parameters from (wrong name) AB to
157        BDF (backward difference time discretisation)
158      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
159    o tools/adjoint_options:
160      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
161    
162    checkpoint64t (2014/02/01)
163    o pkg/ecco
164      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
165        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
166      - replace hard-coded record number and period which only work for monthly
167        with read-in runtime param that works for other periods (month,day,year)
168    o pkg/thsice
169      - corrected store directive fixes thsice adjoint gradient checks
170    o genmake2 & testreport:
171      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
172        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
173        Update testreport accordingly. No need to set "export OPENAD=true"
174        in adjoint_options/adjoint_oad anymore (will be removed later).
175    o pkg/shelfice:
176      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
177        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
178        so that surface forcing applies to k=kSurf if using pkg/shelfice.
179    o pkg/ctrl, pkg/grdchk, pkg/ecco:
180      - Changes to make GENARR more modular (i.e. invisible if not used)
181    o model/src/temp_integrate.F and salt_integrate.F
182      - re-include store directives that were removed on Dec 27th.
183    o model/src/external_forcing_surf.F
184      - add storage directives for EmPmR and PmEpR to avoid recomputation of
185        seaice_model in the adjoint that is problematic when seaice_model is
186        turned off in the adjoint. The resolved issue dated back to July when
187        EXTERNAL_FORCING_SURF call was moved.
188        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
189    o pkg/exf/exf_check.F
190      - fix a small bug again (originally found by Wentao Liu, now found again)
191      - streamline error output
192    o pkg/streamice and aim_v23:
193      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
194        Apple's /usr/bin/cpp knows what to do:
195        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
196        Target: x86_64-apple-darwin13.0.0
197    
198    checkpoint64s (2014/01/05)
199    o tools/adjoint_options:
200      - switch to fastopt.net TAF server (instead of default fastopt.de) for
201        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
202    o model/src:
203      - remove some unnecessary TAF storage directives in forward_step.F and
204        in dynamics.F (note: not always removed by TAF, e.g., double storage
205        of kappaRU,kappaRV in former version of dynamics.F).
206    o model/src & pkg/ptracers:
207      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
208        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
209        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
210      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
211      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
212      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
213    o useSingleCpuInput separates single-CPU input from single-CPU output;
214        for now only implemented for in exf_interp_read.F
215    o verification/advect_xy:
216      - fix missing EXCH call in local version of ini_salt.F and update output.
217    o momentum diagnostics:
218      - fix which deltaT is used in Total-Tendency diagnostics.
219      - fix typo in diagnostics for momentum tendency from AB.
220    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
221        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
222    
223    checkpoint64r (2013/12/08)
224    o verification/*/results:
225      - Update reference output of experiments that were passing with just 13 digits
226         (make it easier to detect future changes in results)
227    o model/src & pkg/ptracers:
228      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
229        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
230        to inside ptracers_integrate.F ; remove ptracers_advection.F
231    o coupling interface pkgs:
232        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
233      - change the config check to test the agreement of Ocean Depth
234        with ATM land/sea mask (instead of ATM orography);
235      - send to coupler the number of coupler time-steps to do for this run:
236        this allows to check for consistency and don't need anymore to be
237        specified in parameter file "data";
238      in coupler:
239      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
240      - improve report to log-file of config setting (pass log-file unit to few S/R)
241    o pkg/compon_communic:
242      - add coupling send/receive for non-tiled integer vector;
243      - add S/R to check and stop if any proc has an error (similar to
244        eesupp/src/stop_if_error.F but single thread and across Comm_World).
245    o pkg/exch2:
246      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
247        through list of all tiles my proc owns.
248    o model/src:
249      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
250        from rTrans) to simplify dependencies (no need to store rTrans anymore in
251        calling S/R); this affects AD results at machine truncation level:
252        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
253        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
254    o tools/build_options:
255      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
256    o coupling interface pkgs:
257        [compon_communic, atm_compon_interf & ocn_compon_interf]
258      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
259        to each S/R that needs it; remove un-used variables.
260      - change component tile registration (cpl_register.F in both compon_interf
261        and mitcomponent_tile_register.F) to pass the full list of tiles
262        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
263      - with pkg/exch2: adopt the same convention used for I/O to define mapping
264        towards coupler global array (unless W2_useE2ioLayOut=F):
265         a) can now use different tiling between atm & ocn comp.
266         b) no needs to modify the run-Off map when changing tiling (was needed
267            even if using the same tiling between atm & ocn).
268         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
269            full land tiles); not yet tested.
270      - check for valid mapping from comp. tile to coupler global array
271      - improve report of tile registration results to log file.
272    o pkg/exch2:
273      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
274        tile-registration (CPL_REGISTER);
275      - activate (un-comment) definition and setting of "W2_tileIndex" list to
276        store the local bi,bj indices of each tile;
277      - also print bi,bj in local report to log file;
278      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
279        Jun 2009 modif of pkg/exch2).
280    o testing on baudelaire:
281      - run 2 tests at a time: no significant slow down (since enough cpu) and
282        get the full set of test done earlier
283      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
284    o model/src/thermodynamics.F and routines called from it:
285      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
286        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
287        velocity (outp) by adding bolus velocity.
288      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
289        mass transport from velocity + lateral grid cell area
290      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
291      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
292     in thermodynamics.F
293      - remove k from thermodynamics.F and move it to temp_integrate.F
294        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
295        loop).
296      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
297        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
298        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
299        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
300      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
301        global_ocean.90x40x15, tutorial_global_oce_biogeo and
302        tutorial_tracer_adjsens (+ TLM output).
303    o tools/OAD_support and (verification/*/) code_oad:
304      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
305        module conversion ; remove unneeded CPP_EEOPTIONS.h.
306      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
307        version (closer to model/inc/CPP_OPTIONS.h).
308    o model/src:
309      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
310        retired list of parameters (routine FREEZE has been replace by surface
311        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
312    o pkg/gmredi:
313      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
314        velocity (same scheme but affects machine truncation) for GM_AdvForm.
315      - update output of FWD experiments: front_relax.bvp,
316        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
317    
318    checkpoint64q (2013/11/17)
319    o verification:
320      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
321        tutorial_global_oce_biogeo and global_ocean.90x40x15.
322      - generate new output (growth & melt) for seaice_itd experiment after
323        updating the input pickup_seaice files (previously wrong).
324    o pkg/cost:
325      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
326        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
327        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
328          cannot be applied to var in common block).
329        o allows to get results independent of tile-per-proc setting (if using
330          slower GLOBAL_SUM_SEND_RECV option).
331      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
332        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
333        forward gradients: update output).
334      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
335        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
336    o pkg/mom_common:
337      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
338        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
339        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
340        ensure that all field value that are used are set.
341    o tutorial_deep_convection (smag3d):
342      - add missing scaling in mom_calc_smag_3d.F;
343      - set smag3D_coeff in input.smag3d such that results do not change.
344    o pkg/dic:
345      - change dic_cost.F to compute cost on each tile first and then apply
346        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
347        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
348      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
349    o eesupp/src & pkg/mdsio:
350      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
351        (from pkg/mdsio) since they are no longer used for tape IO.
352      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
353        (+ keep a copy in pkg/atm_ocn_coupler).
354    o verification/isomip:
355      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
356    o tools/build_options:
357      - optfile linux_amd64_ifort11, fast (no ieee) case:
358        to get a working restart for all experiments, add "-fp-model source"
359        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
360    
361    checkpoint64p (2013/10/20)
362    o pkg/autodiff:
363      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
364        criteria, return to simple (default) tape IO format.
365    o pkg/mdsio (+ eesupp/src):
366      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
367        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
368      - fix globalFile and singleCpuIO options using simpler global mapping.
369      - new pairs of scatter/gather vector S/R (one for each type, generated from
370        template) corresponding to simpler global mapping.
371      - adread_write.F: switch to new S/R (but leave old calls commented) and write
372        to globalFile when parameter globalFiles is set to True.
373      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
374    o pkg/autodiff:
375      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
376        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
377        missing, just add a STOP if array type do not match.
378    o pkg/exf:
379      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
380         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
381         and rename array obsSIce to exf_iceFraction.
382    o tutorial_deep_convection:
383      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
384        for now all in this exp. code dir.
385      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
386        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
387    o eesupp/src:
388      - added SINGLE_DISK_IO option because reading of parameter files on
389        very large number of processors did not work with existing set-up
390    
391    checkpoint64o (2013/09/25)
392    o pkg/atm_phys & atm_compon_interf:
393      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
394    o tools/build_options:
395      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
396        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
397        remove CPP setting (was identical to genmake2 default).
398    o pkg/gmredi & model/src: Some updating and work done on the residual model.
399      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
400      - fixed up the calculation of the eddy stress and how it is added to the
401        external forcing via taueddy_external_forcing.F
402      - at the moment, it is very experimental and only works with the variable eddy
403        diffusivity calculated in gmredi_k3d.F
404    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
405        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
406    o testreport (& tools/do_tst_2+2):
407      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
408    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
409      - remove CPP='cpp -traditional -P' (this is genmake2 default)
410      - add switch (for big setups) to use 'medium' memory-model (but leave it
411        commented out for now). Note: needed with FC 19 to compile big setups.
412    o pkg/atm_compon_interf:
413      - regroup per field origin (model & pkgs) the coupling storage routines
414         (which accumalate in time each coupling field)
415      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
416        update accordingly + simplify aim_do_physics.F
417    
418    checkpoint64n (2013/08/26)
419    o pkg/bbl:
420      - update formulation to reduce dispersion of tracer properties in bbl
421      - replaced horizontal and vertical transport parameters with velocities
422      - changes results for verification/global_with_exf.yearly
423    o verification/halfpipe_streamice:
424      - change to matrix construction; update both Fwd & AD output.
425    o verification/tutorial_tracer_adjsens:
426      - OpenAD test: switch to vector-invariant momentum since fluxform with
427        rStar causes problems with OpenAD; update output.
428    o tools:
429      - genmake2: define a common prefix for all temp-file names ; move them
430        to local /tmp disk (but would be easy to move them back);
431      - xmakedepend: apply the same switch for temp-files.
432    o pkg/offline:
433      - changes for use with rStar (NLFS): assume that we continue to provide
434        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
435        output files) and apply r* scaling at each time-step (function of the time
436        varying Eta field); use normal pickup files (needed for restart with NLFS).
437    o adjoint with OpenAD:
438      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
439        package openad.  This package has to be compiled for all runs with OpenAD
440        instead of specifying code_oad_all as a modification directory.
441      - link the fortran templates from tools/OAD_support to the build directory
442        for preprocessing to avoid conflicts between different setups compiled
443        simultaneously and simplify cleanup.
444    o pkg/exf:
445      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
446        main model or other pkgs are exchanged in EXF_MAPFIELDS).
447    o model/src:
448      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
449        (similar to do_fields_blocking_exchanges.F).
450    o tools/genmake2:
451      - remove TAF output src code just before calling staf (when not doing a fresh
452        built, will stop if things go wrong with staf).
453      - fix target "adobj" (left from TAF version-2 transition)
454    o pkg/diagnostics:
455      - add a parameter to track the status of pkg/diagnostics activation;
456        this replace/extend the use of logical param "settingDiags" (to check
457        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
458        New S/R to print error message and stop when pkgStatus is not right.
459      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
460    
461    checkpoint64m (2013/08/13)
462    o model/inc:
463      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
464        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
465    o pkg/kpp & aim_v23:
466      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
467    o pkg/seaice:
468      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
469        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
470      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
471    o eesupp/src:
472      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
473        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
474    o switch to TAF version-2:
475      - add flow directives to "freeze" naming convention for ad-routines that
476        are used in I/O routines of adjoint state and associated common blocks
477        that are used in adcommon.h (backward compatible with version-1)
478      - update all ad-optfiles (in tools/adjoint_options + few local to some
479        verification exp) to switch to latest TAF version (currently 2.5.5);
480        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
481        out except for diva).
482      - the major change with TAF version-2 is that both the differentiated
483        routines and the forward routines (new) are returned as part of the TAF
484        output source code. Update genmake2 accordingly.
485      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
486        with version-2 when compared to TLM or FWD gradient); other experiments
487        output show minor changes (machine truncation level); update the few AD &
488        TLM output with 12 matching digits only (some prior to version-2 switch).
489    
490    checkpoint64l (2013/08/05)
491    o model/src:
492      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
493      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
494        when using TAF but only if using OpenAD.
495    o pkg/mom_common+fluxform+vecinv:
496      - always set horiz. viscosity arrays to background value before calling
497        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
498        only when using variable horiz. viscosity (useVariableVisc=T);
499      - simplify mom_vecinv.F (only 1 block for momViscosity).
500    o pkg/mom_common: variable horiz. viscosity in NH code
501      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
502        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
503      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
504        useBiharmonicVisc & useVariableVisc.
505      - fix old bug (already in 1rst implementation of variable horizontal viscosity
506        in calc_gw.F, version 1.27, 2006/06/20):
507        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
508        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
509      - change background horiz viscosity in vertical momentum (gW) to always be
510        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
511        any type of variable viscosity, e.g., viscAh/4Grid)
512      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
513        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
514        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
515        default viscAh,viscA4 is zero).
516    o model/src:
517      - extend length of drC & recip_drC from Nr to Nr+1.
518    o Divided Adjoint (DIVA) with MPI:
519      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
520      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
521        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
522    
523    checkpoint64k (2013/07/23)
524    o tools/OAD_support:
525      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
526        and remove it from genmake2.
527    o tools/build_options:
528      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
529        MPI_HEADER_FILES list (let genmake2 find the missing headers)
530    o verification/halfpipe_streamice:
531      - change to driving stress formulation; update both Fwd & AD output.
532    o tools/genmake2 and Divided Adjoint with MPI:
533      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
534      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
535      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
536        Makefile, which is set by genmake2, and check which mpi-headers are needed.
537        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
538      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
539    o testreport:
540      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
541        perform additional runs (number of additional runs is "add_DIVA_runs" taken
542        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
543    o verification/lab_sea (AD test):
544      - change to test Divided Adjoint Run in this set-up (both standard AD test
545        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
546    o pkg atm_ & ocn_compon_interf:
547      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
548        staggerTimeStep implementation) and disable (retired) corresponding
549        parameter.
550    o pkg/offline:
551      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
552      - add S/R OFFLINE_CHECK to print offline parameter summary
553        and stop if loading a file that is not used;
554      - enable to calculate GMRedi tensor, KPP mixing and convective index
555        when the corresponding file(s) is/are not specified (but pkg is used).
556      - comment out resetting of monitorFreq (to endTime) since it still useful
557        for monitoring CFL numbers and checking offline fields.
558    o OpenAD:
559      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
560        smaller standard output) and generate new (smaller) output (on baudelaire
561        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
562    o model/src:
563      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
564        (where external_forcing_adjust was called) and change list of arguments;
565      - merge external_forcing_adjust.F into external_forcing_surf.F
566      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
567        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
568        previously in file "balance_relax.F", now removed); remove corresponding
569        arrays in FFIELDS.h.
570      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
571        a hack for getting back surfaceForcingS (loaded from file) when using
572        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
573      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
574        (was getting only 11 digits for AD-grad, due to different truncation
575         error in AD code).
576    
577    checkpoint64j (2013/07/04)
578    o pkg/offline:
579      - to enable the use of other features with pkg offline (e.g., obcs),
580        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
581      - comment out "allowFreezing" (now active) in 2 offline testing exp.
582    o pkg/exf ALLOW_RUNOFTEMP
583      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
584      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
585      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
586    o pkg/atm_phys:
587      - allows to add some damping on uVel,vVel (strength only function of k).
588    o verification, ad-tests:
589      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
590        global_ocean_ebm and offline_exf_seaice.thsice.
591    o verification/halfpipe_streamice:
592      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
593        flux input boundary conditions to be ignored; a fix for this bug changed
594        verification results for forward test.
595      - add adjoint test.
596    o pkg/ptracers:
597      - allow to restart without SOM pickup (resetting SOM to zero).
598    o pkg/gmredi:
599      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
600      - It uses mixing length theory and suppression by steering level effects to
601        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
602        to JPO, for more details).
603      - It also uses the diffusivity to calculate an eddy induced streamfunction
604        based on a PV closure (rather than a buoyancy closure as in GM).
605      - New files added to pkg/gmredi:
606        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
607          induced overturning streamfunction (called from gmredi_calc_tensor)
608        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
609          for use in gmredi_k3d
610        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
611          the eddy diffusivity
612    
613  checkpoint64i (2013/06/18)  checkpoint64i (2013/06/18)
614  o pkg/cheapaml:  o pkg/cheapaml:
# Line 40  o pkg/cfc: Line 645  o pkg/cfc:
645      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
646    - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf    - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
647    - new routine to print summary of CFC params and check for consistency.    - new routine to print summary of CFC params and check for consistency.
648    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
649      similar to thsice_advdiff.
650      Note that for the B-grid case the routine parameters uc/vc are overwritten.
651  o pkg/cfc:  o pkg/cfc:
652    - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);    - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
653      update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.      update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
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