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revision 1.1859 by dimitri, Tue Apr 23 19:05:16 2013 UTC revision 1.2000 by mlosch, Tue May 27 15:27:14 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/seaice:
8      - remove code that resets useThSice in S/R seaice_readparms and
9        replace by a warning in S/R seaice_check
10      - remove parameter MULTDIM, replace with nITD and runtime
11        parameter SEAICE_multDim (still hard-wired to nITD if
12        SEAICE_ITD is defined)
13    
14    checkpoint64x (2014/05/24)
15    o verification/lab_sea:
16      - update adjoint and TLM output following changes to pkg/salt_plume
17      - un-do the update after putting back local recip_Cp in few places.
18    o pkg/salt_plume: modifications by An Nguyen:
19      - add capability to do brine rejection (salt-plume) as function of
20        volume+tracers (instead of only salinity tracer).
21      - conserve volume by exchanging volume from each kLev to above to
22        accommodate in-coming brine volume
23      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
24      - switch KPP surf buoyancy due to brine forcing to 3-d
25        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
26      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
27      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
28        in East/West Arctic.
29    o pkg/sbo:
30      - incorporate modifications from Katherine Quinn to enable the use of sbo
31        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
32        output for future testreport verification (unfinished).
33    o pkg/atm_phys:
34      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
35        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
36        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
37    o pkg/seaice
38      seaice_calc_ice_strength.F: modify expression to avoid divisions
39        (affects truncation)
40      seaice_do_ridging.F: clean up the insectarium
41      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
42      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
43      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
44      - add some debugging information and error messages (warnings)
45    o model/src: modifications relatd to atmosphere p*:
46      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
47      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
48        of vertical profile tRef in geopotential background and anomaly.
49      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
50        and pkg/atm_phys.
51      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
52        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
53    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
54    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
55        not used right now, but can be used in BGC packages to fix conservation.
56    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
57        other packages too.
58    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
59        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
60    o model/src:
61      - since we have several heat capacity (even in model/src), define "recip_Cp"
62        as local variable (no longer in common block) to avoid any confusion.
63      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
64    o pkg/exf:
65      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
66        air density as function of air Temp, Humidity and atm pressure.
67    
68    checkpoint64w (2014/05/02)
69    o verification:
70      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
71        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
72        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
73        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
74        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
75    o model/src: for atmosphere in p* coords:
76      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
77      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
78        but not yet activated.
79    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
80      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
81      - this changes the results (but not for any verification experiment, because
82        none tests this), but avoids having an extra field in the restart files
83    o pkg/seaice: remove global variable TICE (not needed)
84      - replace by TICES or local variable where necessary (cost_seaice_test,
85        seaice_diagnostics_state)
86      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
87      - use specific read/write routines for reading and writing individual leves
88        of a multilevel field
89    o pkg/ctrl & model/inc:
90      - move additional anomaly fields of control vars (related to options:
91         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
92        from DYNVARS.h into new header file: CTRL_FIELDS.h
93    o pkg/seaice: some small modifications to the ridging code
94      - make fw2ObyRidge a global variable and add the freshwater flux to
95        seaice_growth
96      - pass actual thickness from seaice_prepare_ridging, so that it is
97        computed only in one place and compute it in the same way as in
98        seaice_growth
99      - initialise more fields in seaice_do_ridging that where cause floating
100        point exceptions over land
101    o pkg/seaice: preparations for ridging code and first real ridging code
102      - move most of "PART 1" of S/R seaice_growth into a new and separate
103        S/R seaice_reg_ridge that will both regularize the state variable after
104        advection call the actual ridging routine;
105      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
106        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
107      - remove ridging code from seaice_advdiff
108      - clean up remaining part 1 of seaice_growth in an attempt to make it
109        more readable (this is probably subjective)
110      - call seaice_itd_redist once in the initialisation phase to have the initial
111        conditions in the correct category
112      - finally: add new ridging routine for ITD code
113    
114    checkpoint64v (2014/04/11)
115    o pkg/ecco:
116      - add runtime parameters mdt[start,end]date[1,2]
117      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
118    o pkg/seaice:
119      - make deltaC a global variable, so that it can be used in ridging code
120      - first step towards ridging: introduce new routines that compute
121        ice strength based on ridging parameters
122      - add diagnostic for HSNOWITD
123      - add opnWtrFrac as a global variable (required for ridging scheme)
124    o pkg/salt_plume + pkg/seaice/seaice_growth.F
125      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
126        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
127    o verification/hs94.1x64x5:
128      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
129      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
130    o autodiff:
131      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
132        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
133        For now, only in pkgs used in verification/hs94.1x64x5.
134      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
135        which are specific to TAF/TAMC).
136      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
137        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
138        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
139      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
140        building mitgcmuv_ad (make adAll).
141    o pkg/ecco:
142      - cost_gencost_seaicev4.F:
143         reformulate proxy cost as function of sst and local param SEAICE_freeze
144         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
145      - add stop statement if old names siv4-[sst,vol] are used
146      - add snapshots + cost reports for atmospheric longwave
147      - remove factor 0.1 in front of wtau[u,v]
148      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
149         ALLOW_TMI_SST_COST_CONTRIBUTION
150    o pkg/atm_phys:
151      - add some diagnostics for Short-wave and for convection S/R.
152    o pkg/seaice/seaice_growth:
153      - fix a bug in the lateral melt parameterization for SEAICE_ITD
154        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
155      - rearrange loop order for better vector code in the same code block
156      - rewrite the floeDiameter formula to have fewer divisions
157      -  (miraculously) none of this changes the results of seaice_itd
158    o pkg/smooth:
159      - move param smooth2Ddiffnbt to pkg/ecco
160    o pkg/salt_plume:
161      - salt_plume_frac.F:
162         clean up local param names
163         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
164    o pkg/rw:
165      - add RS version of S/R READ_MFLDS_LEV.
166    o pkg/streamice:
167      - fix the restart test by writing/reading pickup_streamice files.
168    o pkg/seaice:
169      - refine checks for jfnk-related parameters
170      - comment out if statement with SEAICEuseIMEX parameter as long as there
171        is no IMEX code to avoid confusion and surprises
172    
173    checkpoint64u (2014/03/07)
174    o verification/MLAdjust:
175      - rename secondary test suffix:
176         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
177         0.leithD -> AhFlxF  + switch to flux-form
178         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
179         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
180    o pkg/mom_vecinv:
181      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
182        to be before mom_calc_visc.F)
183      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
184      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
185        this is simpler for the adjoint and for diagnostics.
186    o model/src + pkg/momentum:
187      - add input files for  2-D additional Western and Southern cell-edge wall
188         (e.g., to add "thin-wall" where it is =1).
189      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
190        using 2nd hFacZ that is computed from initial (fix domain) hFac
191      - known limitations of thin wall implementation: not yet coded for sigma
192        coords; not working with CD-scheme neither.
193    o pkg/seaice:
194      - rename recently introduced parameters from (wrong name) AB to
195        BDF (backward difference time discretisation)
196      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
197    o tools/adjoint_options:
198      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
199    
200    checkpoint64t (2014/02/01)
201    o pkg/ecco
202      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
203        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
204      - replace hard-coded record number and period which only work for monthly
205        with read-in runtime param that works for other periods (month,day,year)
206    o pkg/thsice
207      - corrected store directive fixes thsice adjoint gradient checks
208    o genmake2 & testreport:
209      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
210        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
211        Update testreport accordingly. No need to set "export OPENAD=true"
212        in adjoint_options/adjoint_oad anymore (will be removed later).
213    o pkg/shelfice:
214      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
215        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
216        so that surface forcing applies to k=kSurf if using pkg/shelfice.
217    o pkg/ctrl, pkg/grdchk, pkg/ecco:
218      - Changes to make GENARR more modular (i.e. invisible if not used)
219    o model/src/temp_integrate.F and salt_integrate.F
220      - re-include store directives that were removed on Dec 27th.
221    o model/src/external_forcing_surf.F
222      - add storage directives for EmPmR and PmEpR to avoid recomputation of
223        seaice_model in the adjoint that is problematic when seaice_model is
224        turned off in the adjoint. The resolved issue dated back to July when
225        EXTERNAL_FORCING_SURF call was moved.
226        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
227    o pkg/exf/exf_check.F
228      - fix a small bug again (originally found by Wentao Liu, now found again)
229      - streamline error output
230    o pkg/streamice and aim_v23:
231      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
232        Apple's /usr/bin/cpp knows what to do:
233        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
234        Target: x86_64-apple-darwin13.0.0
235    
236    checkpoint64s (2014/01/05)
237    o tools/adjoint_options:
238      - switch to fastopt.net TAF server (instead of default fastopt.de) for
239        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
240    o model/src:
241      - remove some unnecessary TAF storage directives in forward_step.F and
242        in dynamics.F (note: not always removed by TAF, e.g., double storage
243        of kappaRU,kappaRV in former version of dynamics.F).
244    o model/src & pkg/ptracers:
245      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
246        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
247        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
248      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
249      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
250      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
251    o useSingleCpuInput separates single-CPU input from single-CPU output;
252        for now only implemented for in exf_interp_read.F
253    o verification/advect_xy:
254      - fix missing EXCH call in local version of ini_salt.F and update output.
255    o momentum diagnostics:
256      - fix which deltaT is used in Total-Tendency diagnostics.
257      - fix typo in diagnostics for momentum tendency from AB.
258    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
259        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
260    
261    checkpoint64r (2013/12/08)
262    o verification/*/results:
263      - Update reference output of experiments that were passing with just 13 digits
264         (make it easier to detect future changes in results)
265    o model/src & pkg/ptracers:
266      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
267        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
268        to inside ptracers_integrate.F ; remove ptracers_advection.F
269    o coupling interface pkgs:
270        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
271      - change the config check to test the agreement of Ocean Depth
272        with ATM land/sea mask (instead of ATM orography);
273      - send to coupler the number of coupler time-steps to do for this run:
274        this allows to check for consistency and don't need anymore to be
275        specified in parameter file "data";
276      in coupler:
277      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
278      - improve report to log-file of config setting (pass log-file unit to few S/R)
279    o pkg/compon_communic:
280      - add coupling send/receive for non-tiled integer vector;
281      - add S/R to check and stop if any proc has an error (similar to
282        eesupp/src/stop_if_error.F but single thread and across Comm_World).
283    o pkg/exch2:
284      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
285        through list of all tiles my proc owns.
286    o model/src:
287      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
288        from rTrans) to simplify dependencies (no need to store rTrans anymore in
289        calling S/R); this affects AD results at machine truncation level:
290        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
291        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
292    o tools/build_options:
293      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
294    o coupling interface pkgs:
295        [compon_communic, atm_compon_interf & ocn_compon_interf]
296      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
297        to each S/R that needs it; remove un-used variables.
298      - change component tile registration (cpl_register.F in both compon_interf
299        and mitcomponent_tile_register.F) to pass the full list of tiles
300        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
301      - with pkg/exch2: adopt the same convention used for I/O to define mapping
302        towards coupler global array (unless W2_useE2ioLayOut=F):
303         a) can now use different tiling between atm & ocn comp.
304         b) no needs to modify the run-Off map when changing tiling (was needed
305            even if using the same tiling between atm & ocn).
306         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
307            full land tiles); not yet tested.
308      - check for valid mapping from comp. tile to coupler global array
309      - improve report of tile registration results to log file.
310    o pkg/exch2:
311      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
312        tile-registration (CPL_REGISTER);
313      - activate (un-comment) definition and setting of "W2_tileIndex" list to
314        store the local bi,bj indices of each tile;
315      - also print bi,bj in local report to log file;
316      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
317        Jun 2009 modif of pkg/exch2).
318    o testing on baudelaire:
319      - run 2 tests at a time: no significant slow down (since enough cpu) and
320        get the full set of test done earlier
321      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
322    o model/src/thermodynamics.F and routines called from it:
323      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
324        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
325        velocity (outp) by adding bolus velocity.
326      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
327        mass transport from velocity + lateral grid cell area
328      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
329      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
330     in thermodynamics.F
331      - remove k from thermodynamics.F and move it to temp_integrate.F
332        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
333        loop).
334      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
335        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
336        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
337        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
338      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
339        global_ocean.90x40x15, tutorial_global_oce_biogeo and
340        tutorial_tracer_adjsens (+ TLM output).
341    o tools/OAD_support and (verification/*/) code_oad:
342      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
343        module conversion ; remove unneeded CPP_EEOPTIONS.h.
344      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
345        version (closer to model/inc/CPP_OPTIONS.h).
346    o model/src:
347      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
348        retired list of parameters (routine FREEZE has been replace by surface
349        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
350    o pkg/gmredi:
351      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
352        velocity (same scheme but affects machine truncation) for GM_AdvForm.
353      - update output of FWD experiments: front_relax.bvp,
354        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
355    
356    checkpoint64q (2013/11/17)
357    o verification:
358      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
359        tutorial_global_oce_biogeo and global_ocean.90x40x15.
360      - generate new output (growth & melt) for seaice_itd experiment after
361        updating the input pickup_seaice files (previously wrong).
362    o pkg/cost:
363      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
364        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
365        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
366          cannot be applied to var in common block).
367        o allows to get results independent of tile-per-proc setting (if using
368          slower GLOBAL_SUM_SEND_RECV option).
369      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
370        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
371        forward gradients: update output).
372      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
373        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
374    o pkg/mom_common:
375      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
376        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
377        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
378        ensure that all field value that are used are set.
379    o tutorial_deep_convection (smag3d):
380      - add missing scaling in mom_calc_smag_3d.F;
381      - set smag3D_coeff in input.smag3d such that results do not change.
382    o pkg/dic:
383      - change dic_cost.F to compute cost on each tile first and then apply
384        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
385        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
386      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
387    o eesupp/src & pkg/mdsio:
388      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
389        (from pkg/mdsio) since they are no longer used for tape IO.
390      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
391        (+ keep a copy in pkg/atm_ocn_coupler).
392    o verification/isomip:
393      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
394    o tools/build_options:
395      - optfile linux_amd64_ifort11, fast (no ieee) case:
396        to get a working restart for all experiments, add "-fp-model source"
397        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
398    
399    checkpoint64p (2013/10/20)
400    o pkg/autodiff:
401      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
402        criteria, return to simple (default) tape IO format.
403    o pkg/mdsio (+ eesupp/src):
404      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
405        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
406      - fix globalFile and singleCpuIO options using simpler global mapping.
407      - new pairs of scatter/gather vector S/R (one for each type, generated from
408        template) corresponding to simpler global mapping.
409      - adread_write.F: switch to new S/R (but leave old calls commented) and write
410        to globalFile when parameter globalFiles is set to True.
411      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
412    o pkg/autodiff:
413      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
414        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
415        missing, just add a STOP if array type do not match.
416    o pkg/exf:
417      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
418         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
419         and rename array obsSIce to exf_iceFraction.
420    o tutorial_deep_convection:
421      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
422        for now all in this exp. code dir.
423      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
424        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
425    o eesupp/src:
426      - added SINGLE_DISK_IO option because reading of parameter files on
427        very large number of processors did not work with existing set-up
428    
429    checkpoint64o (2013/09/25)
430    o pkg/atm_phys & atm_compon_interf:
431      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
432    o tools/build_options:
433      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
434        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
435        remove CPP setting (was identical to genmake2 default).
436    o pkg/gmredi & model/src: Some updating and work done on the residual model.
437      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
438      - fixed up the calculation of the eddy stress and how it is added to the
439        external forcing via taueddy_external_forcing.F
440      - at the moment, it is very experimental and only works with the variable eddy
441        diffusivity calculated in gmredi_k3d.F
442    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
443        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
444    o testreport (& tools/do_tst_2+2):
445      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
446    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
447      - remove CPP='cpp -traditional -P' (this is genmake2 default)
448      - add switch (for big setups) to use 'medium' memory-model (but leave it
449        commented out for now). Note: needed with FC 19 to compile big setups.
450    o pkg/atm_compon_interf:
451      - regroup per field origin (model & pkgs) the coupling storage routines
452         (which accumalate in time each coupling field)
453      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
454        update accordingly + simplify aim_do_physics.F
455    
456    checkpoint64n (2013/08/26)
457    o pkg/bbl:
458      - update formulation to reduce dispersion of tracer properties in bbl
459      - replaced horizontal and vertical transport parameters with velocities
460      - changes results for verification/global_with_exf.yearly
461    o verification/halfpipe_streamice:
462      - change to matrix construction; update both Fwd & AD output.
463    o verification/tutorial_tracer_adjsens:
464      - OpenAD test: switch to vector-invariant momentum since fluxform with
465        rStar causes problems with OpenAD; update output.
466    o tools:
467      - genmake2: define a common prefix for all temp-file names ; move them
468        to local /tmp disk (but would be easy to move them back);
469      - xmakedepend: apply the same switch for temp-files.
470    o pkg/offline:
471      - changes for use with rStar (NLFS): assume that we continue to provide
472        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
473        output files) and apply r* scaling at each time-step (function of the time
474        varying Eta field); use normal pickup files (needed for restart with NLFS).
475    o adjoint with OpenAD:
476      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
477        package openad.  This package has to be compiled for all runs with OpenAD
478        instead of specifying code_oad_all as a modification directory.
479      - link the fortran templates from tools/OAD_support to the build directory
480        for preprocessing to avoid conflicts between different setups compiled
481        simultaneously and simplify cleanup.
482    o pkg/exf:
483      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
484        main model or other pkgs are exchanged in EXF_MAPFIELDS).
485    o model/src:
486      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
487        (similar to do_fields_blocking_exchanges.F).
488    o tools/genmake2:
489      - remove TAF output src code just before calling staf (when not doing a fresh
490        built, will stop if things go wrong with staf).
491      - fix target "adobj" (left from TAF version-2 transition)
492    o pkg/diagnostics:
493      - add a parameter to track the status of pkg/diagnostics activation;
494        this replace/extend the use of logical param "settingDiags" (to check
495        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
496        New S/R to print error message and stop when pkgStatus is not right.
497      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
498    
499    checkpoint64m (2013/08/13)
500    o model/inc:
501      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
502        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
503    o pkg/kpp & aim_v23:
504      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
505    o pkg/seaice:
506      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
507        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
508      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
509    o eesupp/src:
510      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
511        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
512    o switch to TAF version-2:
513      - add flow directives to "freeze" naming convention for ad-routines that
514        are used in I/O routines of adjoint state and associated common blocks
515        that are used in adcommon.h (backward compatible with version-1)
516      - update all ad-optfiles (in tools/adjoint_options + few local to some
517        verification exp) to switch to latest TAF version (currently 2.5.5);
518        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
519        out except for diva).
520      - the major change with TAF version-2 is that both the differentiated
521        routines and the forward routines (new) are returned as part of the TAF
522        output source code. Update genmake2 accordingly.
523      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
524        with version-2 when compared to TLM or FWD gradient); other experiments
525        output show minor changes (machine truncation level); update the few AD &
526        TLM output with 12 matching digits only (some prior to version-2 switch).
527    
528    checkpoint64l (2013/08/05)
529    o model/src:
530      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
531      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
532        when using TAF but only if using OpenAD.
533    o pkg/mom_common+fluxform+vecinv:
534      - always set horiz. viscosity arrays to background value before calling
535        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
536        only when using variable horiz. viscosity (useVariableVisc=T);
537      - simplify mom_vecinv.F (only 1 block for momViscosity).
538    o pkg/mom_common: variable horiz. viscosity in NH code
539      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
540        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
541      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
542        useBiharmonicVisc & useVariableVisc.
543      - fix old bug (already in 1rst implementation of variable horizontal viscosity
544        in calc_gw.F, version 1.27, 2006/06/20):
545        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
546        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
547      - change background horiz viscosity in vertical momentum (gW) to always be
548        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
549        any type of variable viscosity, e.g., viscAh/4Grid)
550      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
551        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
552        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
553        default viscAh,viscA4 is zero).
554    o model/src:
555      - extend length of drC & recip_drC from Nr to Nr+1.
556    o Divided Adjoint (DIVA) with MPI:
557      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
558      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
559        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
560    
561    checkpoint64k (2013/07/23)
562    o tools/OAD_support:
563      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
564        and remove it from genmake2.
565    o tools/build_options:
566      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
567        MPI_HEADER_FILES list (let genmake2 find the missing headers)
568    o verification/halfpipe_streamice:
569      - change to driving stress formulation; update both Fwd & AD output.
570    o tools/genmake2 and Divided Adjoint with MPI:
571      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
572      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
573      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
574        Makefile, which is set by genmake2, and check which mpi-headers are needed.
575        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
576      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
577    o testreport:
578      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
579        perform additional runs (number of additional runs is "add_DIVA_runs" taken
580        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
581    o verification/lab_sea (AD test):
582      - change to test Divided Adjoint Run in this set-up (both standard AD test
583        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
584    o pkg atm_ & ocn_compon_interf:
585      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
586        staggerTimeStep implementation) and disable (retired) corresponding
587        parameter.
588    o pkg/offline:
589      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
590      - add S/R OFFLINE_CHECK to print offline parameter summary
591        and stop if loading a file that is not used;
592      - enable to calculate GMRedi tensor, KPP mixing and convective index
593        when the corresponding file(s) is/are not specified (but pkg is used).
594      - comment out resetting of monitorFreq (to endTime) since it still useful
595        for monitoring CFL numbers and checking offline fields.
596    o OpenAD:
597      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
598        smaller standard output) and generate new (smaller) output (on baudelaire
599        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
600    o model/src:
601      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
602        (where external_forcing_adjust was called) and change list of arguments;
603      - merge external_forcing_adjust.F into external_forcing_surf.F
604      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
605        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
606        previously in file "balance_relax.F", now removed); remove corresponding
607        arrays in FFIELDS.h.
608      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
609        a hack for getting back surfaceForcingS (loaded from file) when using
610        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
611      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
612        (was getting only 11 digits for AD-grad, due to different truncation
613         error in AD code).
614    
615    checkpoint64j (2013/07/04)
616    o pkg/offline:
617      - to enable the use of other features with pkg offline (e.g., obcs),
618        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
619      - comment out "allowFreezing" (now active) in 2 offline testing exp.
620    o pkg/exf ALLOW_RUNOFTEMP
621      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
622      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
623      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
624    o pkg/atm_phys:
625      - allows to add some damping on uVel,vVel (strength only function of k).
626    o verification, ad-tests:
627      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
628        global_ocean_ebm and offline_exf_seaice.thsice.
629    o verification/halfpipe_streamice:
630      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
631        flux input boundary conditions to be ignored; a fix for this bug changed
632        verification results for forward test.
633      - add adjoint test.
634    o pkg/ptracers:
635      - allow to restart without SOM pickup (resetting SOM to zero).
636    o pkg/gmredi:
637      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
638      - It uses mixing length theory and suppression by steering level effects to
639        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
640        to JPO, for more details).
641      - It also uses the diffusivity to calculate an eddy induced streamfunction
642        based on a PV closure (rather than a buoyancy closure as in GM).
643      - New files added to pkg/gmredi:
644        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
645          induced overturning streamfunction (called from gmredi_calc_tensor)
646        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
647          for use in gmredi_k3d
648        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
649          the eddy diffusivity
650    
651    checkpoint64i (2013/06/18)
652    o pkg/cheapaml:
653      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
654        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
655        with pkg/cheapaml.
656    o utils/python: add subpackage for cubed sphere function, first example is
657        simple cs.pcol to plot 2D fields on a map
658    o pkg/streamice:
659      - This is a new package in MITgcm, which solves dynamic equations for ice
660         sheets and ice streams
661      - At the moment it is independent of atmosphere/ocean dynamics, or any
662        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
663        ed that this will change)
664      - There is a new verification exercise that tests it, halfpipe_streamice,
665        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
666        rectangular embayment
667      - halfpipe_streamice is forward-only for now, will have TAF test soon
668      - for questions, email dgoldber@mit.edu
669    o pkg/thsice:
670      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
671        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
672      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
673         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
674      - allow precip from pkg/cheapaml to make snow over seaice.
675    o pkg/cfc:
676      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
677      - remove atmos CFC 2-D arrays from common bloc (now local variables)
678      - change some hard-coded constant to run time parameter for reading and
679        and interpolating atmospheric CFC ; keep same default as previously.
680      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
681      - put arguments in standard order: myTime, myIter, myThid
682      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
683        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
684      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
685      - new routine to print summary of CFC params and check for consistency.
686    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
687      similar to thsice_advdiff.
688      Note that for the B-grid case the routine parameters uc/vc are overwritten.
689    o pkg/cfc:
690      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
691        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
692      - fix interpolation of atmphspheric CFC between Sorthern and Northern
693        hemisphere value.
694    o pkg/seaice:
695      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
696    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
697                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
698      - requires an additional time level that is stored in the pickup
699      - you can start with AB2 from a pickup without this time level with
700        pickupStrictlyMatch = .false.
701    
702    checkpoint64h (2013/05/26)
703    o pkg/cheapaml:
704      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
705        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
706      - consistent treatment of uWind,vWind location: assume everywhere in
707        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
708        (Note: was already the case for Tair,Qair advection);
709        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
710      - compute diabatic forcing only in the interior (excluding overlap regions)
711      - fill in array "Qsw" (for short-wave heating);
712      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
713        before any update (consistent with MITgcm state var diagnostics);
714      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
715        non periodic ; + adjusted for uWind,vWind (C-grid).
716    o pkg/seaice:
717      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
718        add explicitly pkg/exf in experiments that currently use pkg/seaice.
719      - allows to compile pkg/seaice without pkg/exf.
720    o tools/OAD_support:
721      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
722        of array "ourStepOf" in function rvNextAction (revolve.F90).
723    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
724      - change pkg name (to be used with other atmospheric physics pkg)
725        but by-pass CVS when making the new pkg so that we keep the CVS history.
726    o pkg/offline:
727      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
728        (previously called from pkg/dic_surfforcing_init.F)
729    o model/src:
730      - re-order sequence of calls within packages_init_variables.F, using
731        standard order, except for:
732         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
733         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
734    o new pkg: atm_phys
735      - add entry point and source code (previously in contrib
736          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
737        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
738      - re-order sequence of calls within packages_readparms.F,
739         packages_init_fixed.F and packages_write_pickup.F
740        (but skip packages_init_variables.F because of TAF issues).
741      - update contrib/*/atm_gray/ experiment.
742    o pkg/seaice (ITD code):
743      - simplify and fix the writing of pickup-files for ITD case
744    o pkg/seaice (ITD code):
745      - introduce floe size dependent lateral melt for ITD case;
746      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
747      - update seaice_itd experiment main output.
748    o pkg/thsice:
749      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
750        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
751        changed accordingly pkg/atm2d.
752    
753    checkpoint64g (2013/05/01)
754  o pkg/exf ALLOW_RUNOFTEMP  o pkg/exf ALLOW_RUNOFTEMP
755    - if defined,  river and glacier runoff temperature can be read-in from    - if defined,  river and glacier runoff temperature can be read-in from
756      runoftempfile; runoftempfile needs to have same format as runofffile      runoftempfile; runoftempfile needs to have same format as runofffile
# Line 14  o pkg/thsice (& pkg/bulk_force): Line 761  o pkg/thsice (& pkg/bulk_force):
761    - fix bug (wrong overlap) when using EXF and stressReduction > 0.    - fix bug (wrong overlap) when using EXF and stressReduction > 0.
762  o verification/tutorial_global_oce_biogeo:  o verification/tutorial_global_oce_biogeo:
763    - add preliminary OpenAD setup (still has problems)    - add preliminary OpenAD setup (still has problems)
764    o pkg/seaice:
765      - turn some parameters for choosing the convergence criterion of
766        the inexact Newton method (JFNK) into runtime parameters for convenience
767      - clean up seaice_calc_viscosities.F: remove/retire two options for
768        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
769        the results of lab_sea/input because a division has been replaced by
770        a multiplication with the reciprocal (sumNorm)
771      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
772        convergence of solver (changes results, of course), and to test some
773        new features
774  o model/src:  o model/src:
775    - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.    - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
776    - remove unused forcing field "dQdT" and associated parameter "dQdTFile".    - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
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