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revision 1.1304 by mlosch, Sat Sep 25 23:10:51 2010 UTC revision 1.1460 by jmc, Tue Jun 21 16:17:31 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint62z (2011/06/21)
8    o adjoint monitor:
9     - Add adjoint monitor output for packages exf, seaice
10       and update relevant testreport output
11    o pkg/seaice:
12     - re-order diags inits so that they appear in order in available_diagnostics.log
13     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
14       area/heff/hsnow preceeding thermodynamic growth/melt.
15     - modified diag: SIdA; output actual effect, as the description states.
16     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
17     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
18       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
19        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
20     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
21     - added diagnostics for seaice generic tracers (SItr*).
22     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
23     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
24     I. Fenty: 18-Jun-2011:
25     Minor changes to seaice package:
26     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
27        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
28       - Differentiated "regularization variables" from "floor variables"
29        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
30        * hiceMin became SEAICE_hice_reg (old hiceMin)
31          (with _reg meaning regularization variable)
32       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
33        so as to ensure energy conservation when going between phases
34      - A22 was not used anywhere
35     2) Changed regularization procedure for heffActual and hsnowActual to ensure
36        well-boundedness and smooth adjoint in seaice_growth.F
37     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
38        because the old regularization always set heffActual >= 0.05 cm
39     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
40        on AREA when HEFF > 0.
41      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
42        requiring that DISABLE_AREA_FLOOR *not* be defined
43     Affected verifications:
44      - 1D_ocean_ice_column (output.txt output_adm.txt)
45      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
46    o pkg/diagnostics:
47      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
48      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
49        (was _RL, now integer) with option = 0 to retrieve all levels.
50      - add pieces of code to compute velocity potential at each level (new diagnostics
51        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
52        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
53      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
54        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
55        and in diagnostics_fract_fill.F (do not need a valid pointer for the
56        diagnostics counter-mate); check that definition of counter-diagnostic
57        includes a valid counter-mate (in diagnostics_set_levels.F).
58    o model/src (rStar):
59      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
60        affect solution only if z* with full pressure in EOS;
61        update output of test-exp global_ocean.90x40x15.
62    o pkg/seaice:
63      - introduce siEps=1e-5 parameter
64      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
65      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
66      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
67        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
68        as well as ice cover age and ridging index (attached to AREA).
69        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
70        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
71        Up to SItrMaxNum=3 tracers can be used simultaneously.
72    o pkg/salt_plume:
73      -introduce SPsalFRAC run time parameter that sets the fraction of the
74       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
75       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
76    o model debug options:
77      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
78        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
79      - Refine debug-msg printing selection (3 new levels):
80        debugMode  : controls printing of debug messages (sequence of S/R calls).
81        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
82         debLevZero =  0 ; /* level of disabled aux. msg printing */
83         debLevA =  1 ; /* level of minimum  aux. msg printing */
84         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
85         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
86         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
87         debLevE =  5 ; /* level of extensive debug printing */
88        New debugLevel default: with default debugMode value (=F),
89          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
90          and if debugMode=T, default debugLevel = 4 (debLevD).
91        Relation with previous settings:
92         debLevB (=2) corresponds to former debLevA (=1)
93         debLevD (=4) corresponds to former debLevB (=2)
94        Note:
95         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
96         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
97            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
98      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
99        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
100    o pkg/obcs:
101      - change OBCSfixTopo default from True to False (should not change the results);
102        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
103    o pkg/thsice:
104      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
105        2nd layer seaice sublimation (unlikely to happen)
106      - use Interior mask for OBCS in thsice_advection.F (similar to what is
107        done in gad_advection & seaice_advection).
108    o adjoint:
109      bug fix spotted by Gael Forget:
110      seaice_advection and thsice_advection still had
111      legacy CPP options to avoid CS corner updates for adjoint
112    o pkg/seaice:
113      => Change some of the defaults (2011/05/29):
114         - change SEAICEuseFluxForm default (from False to True)
115         - change DIFF1 default (from 0.004 m/s to 0. m/s)
116         And print warnings if DIFF1 is not set in data.seaice and centered
117          avection scheme is used without any diffusion.
118      also:
119      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
120      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
121      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
122        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
123        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
124      update results of test exp.:
125         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
126             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
127             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
128         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
129         seaice_obcs: output (SEAICEuseFluxForm=T)
130      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
131          for standard fwd & AD lab_sea tests (to keep the same output).
132    o pkg/seaice/seaice_growth.F:
133      - use Ian Fenty's capping formulas for actual ice
134      thickness thoughout EVOLUTION branch.
135      - put treatment pathological case #2) in CPP brackets
136      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
137      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
138    o pkg/seaice:
139      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
140      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
141      also pass fac as a param, which can be 1. (to update the tendency
142      field) or the time step (to update the field itself).
143      - seaice_advdiff.F: for multidim, call seaice_diffusion with
144      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
145      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
146      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
147      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
148    o pkg/seaice:
149      diffusion with centered advection scheme (diffus.F & advect.F):
150      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
151        to just compute the laplacian of input-field.
152      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
153      - fix flux-form version in diffus.F to conserve tracer.
154      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
155       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
156    
157    checkpoint62y (2011/05/26)
158    o pkg/seaice:
159     - seaice_growth.F : in EVOLUTION branch, always include
160       a_QSWbyATM_cover in qnet (as it should be).
161     - verification/global_ocean.cs32x15 : update results accordingly
162       (output.seaice.txt output_adm.seaice.txt).
163    o pkg/seaice + obcs:
164     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
165       equivalent of assuming no tracer gradient outside the OB region.
166       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
167     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
168       after changes above);
169     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
170       only at OB location (instead of over a band of OLx width).
171    o pkg/seaice:
172     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
173       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
174    o pkg/obcs:
175      - split header file "OBCS.h" into 4 separated files:
176        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
177       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
178         (contain no conditional statement which depends on OBCS options).
179      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
180        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
181    o ctrl, cost, grdchk & autodiff pkgs:
182      - make options file more standard (like other {PKG}_OPTIONS.h file but
183        with AD_CONFIG.h); clean-up some of the included header files.
184    o pkg/obcs:
185      - do not mask tracer when applying OB (tracer == 0 could generate problems)
186      - apply tracer OB values to tracer field only at OB location (instead of
187        over a band of OLx width)
188      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
189      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
190        obcs_apply_tloc.F & obcs_apply_sloc.F
191    o obcs in model/src:
192      - call OBCS_APPLY_W only if NonHydrostatic.
193      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
194      - reset dEtaHdt and wVel to zero outside OB interior region ;
195      - leave tracer unchanged outside OB interior region: This has no effect
196        on the solution but just to prevent unrealistic tracer value outside OB.
197      - zero out velocity outside OB interior region: This has no effect on
198        the solution but just to prevent unrealistic velocity outside OB.
199    o obcs and non-lin free-surf:
200       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
201       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
202       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
203       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
204       update results of test-exp. exp4(nlfs).
205    o exp4 (nlfs) test-exp:
206       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
207       with NonLin-FreeSurf); update output.nlfs.txt
208    o obcs and 2d/3d solver norm:
209       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
210       and outside OB interior region (will allow to place OB further inside the
211       domain). Depending on the domain, can affects cg2d-Norm (previous
212       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
213       and cg3d-Norm (previous Norm was computed before canceling OB terms),
214       e.g. in tutorial_plume_on_slope.
215      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
216    o pkg rbcs:
217      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
218      - add capability to apply relaxation to horizontal velocity uVel & vVel.
219    o pkg/grdchk: add gradient check for control variable xx_shifwflx
220    o pkg/shelfice/shelfice_init_fixed.F
221      fix CPP-flag combinations
222    o pkg/seaice: Merge iceage code of Pierre Rampal
223      * update/change/correct ice age calculations
224      * add age updates for pathological cases
225      Probably needs more testing...
226    
227    checkpoint62x (2011/05/13)
228    o pkg/mom_vecinv:
229       high-order vorticity scheme: use interior masks (maskInW & S)
230       to zero-out (outside OB) gradient of vorticity.
231    o verification exp.:
232       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
233       hs94.128x64x5 and seaice_obcs ; update results.
234    o pkg/obcs:
235      fix bug in OBeta for YZ sections in obcs_exf_load.F
236    o pkg/ctrl, pkg/shelfice, and optim:
237      - add new control variable xx_shifwflx (fresh water flux underneath ice
238        shelves). This is almost as tedious as obcs-ctrl, because the
239        variables needs its own mask.
240      - add a cost function term that penalizes the deviation of xx_shifwflx
241        from the first guess (zero) in analogy to other control variables
242    o pkg/shelfice:
243      - start basic adjoint
244    o pkg/ctrl:
245      - remove extra 2D field "for good measure" when initializing in
246        ctrl_set_globfld_[xy/xz/yz].F
247      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
248      - improve error messages in ctrl_set_unpack_*
249    o OBC implementation in momentum:
250       use interior masks (maskInC,W & S) in momentum S/R:
251       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
252       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
253       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
254       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
255       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
256        (and also with Leith/Smagorinsky harmonic-viscosity).
257       Update output of experiment dome and exp4 (+nlfs).
258    o exp4 test-exp:
259      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
260        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
261        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
262        time-varying OB at Western-side for wVel (NonHyd); update output.
263      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
264        and biharmonic-viscosity ; also use prescribed time varying OB.
265    o pkg/obcs:
266      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
267    o model/src:
268      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
269      - initialise startTime & nIter0 with unlikely values: allows to set one
270        from the other without ambiguity.
271    o seaice_obcs test-exp.:
272      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
273    o pkg/obcs:
274      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
275        no longer needed with maskInC,W,S in pkg/generic_advdiff.
276    o pkg/seaice:
277      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
278        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
279      - fixed bug in the initialization of sea ice salinity variable HSALT
280        in seaice_init_varia.F  (removed dependence on ICE2WATR)
281    o fizhi-cs test exp.:
282       switch reference output convention for these 2 non-standard test-exp,
283        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
284          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
285       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
286    o model/inc:
287      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
288        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
289    o pkg/seaice:
290      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
291    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
292      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
293        and initial HSALT
294    
295    checkpoint62w (2011/04/26)
296    o pkg/mom_fluxform:
297      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
298      - use parameter "sideDragFactor" in no-slip BC side-drag part.
299      - update output of exp. global_ocean.90x40x15
300    o pkg/mom_vecinv:
301      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
302    o update seaice exp.:
303      use more consistent parameter values (remove "backward compatability only":
304       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
305      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
306       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
307    o update test-exp global_ocean.90x40x15:
308      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
309      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
310      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
311      o turn on zStar & viscA4 in standard set-up (dir input/)
312        and update output files: output.txt & output.dwnslp.txt
313    o new AD-test experiment: obcs_ctrl
314      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
315    o pkg/dic:
316      fix two bugs in handling water vapour pressure in carbonate chemistry
317      and air-sea fluxes. Found by Val Bennington and Galen McKinley
318      (add DIC Option = WATERVAP_BUG to recover old results)
319      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
320    o adding allowInteriorFreezing option to check for water below freezing point
321      at depth and bring the negative heat anomaly to the surface level
322    o pkgs _fields_load:
323      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
324      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
325        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
326        rbcs to get interpolation weights and time reccord number.
327      - fix multi-threading in aim_fields_load.F
328      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
329    o external_fields_load:
330      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
331       interpolation weights) to use in a periodic time-series ; do not divide by
332       time-step to convert to integer:
333       - this fixes case where externForcingPeriod is not multiple of time-step
334          (Thanks to Christopher L. Wolfe)
335       - this fixes case where externForcingPeriod is an odd multiple of time-step
336         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
337      store index of time-record which is currently loaded:
338       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
339       - needed for the adjoint but not yet used because of extensive recomputations;
340         (to be fixed soon)
341    
342    checkpoint62v (2011/04/02)
343    o verification/1D_ocean_ice_column added to test Ian Fenty's
344      pkg/seaice_growth.F modifications for improving sea ice code differentiability
345    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
346      (new velocity statistics after changing maskInW & maskInS definition)
347    o pkg/generic_advdiff with OBCS:
348      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
349      equivalent to assumption of no tracer gradient outside the OB region.
350      This will affect the results if using obcs+biharmonic diffusion.
351      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
352    o pkg/obcs:
353      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
354      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
355      in Interior region. No impact on solution but affects Velocity monitor stats.
356    o pkg/ptracers (adjoint)
357      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
358      tape file for each tracer
359    o model/inc/src and pkg/autodiff: add parameters that allow to turn
360      of parts of the adjoint code at run time. For now, there are only
361      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
362      parameters are set in data.pkg.
363      This is the lazy coward's version of doing this, but still useful for
364      debugging. In order to do it right, everything needs to be moved to
365      pkg/autodiff.
366    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
367      the end; this fixes the adjoint balancing code for open boundaries.
368    o pkg/ctrl:
369      - change behavior of xx_${varname}period to be analogous to exf-conventions:
370        xx_${varname}period =   0.,  means time-independent control part
371        xx_${varname}period = -12., means one-year-periodic monthly control part
372      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
373        clean up ctrl_init a little, remove unused variables
374      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
375      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
376    
377    checkpoint62u (2011/03/15)
378    o model/src:
379      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
380        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
381      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
382        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
383    o pkg/ctrl/obcs/ecco:
384      - remove obsolete, unused, and partially broken code:
385        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
386        ALLOW_CTRL_OBCS_BALANCE
387      - put a stop statement into ecco/cost_obcsvol.F, but also add
388        cost_obcsvol to ecco_ad_diff.list
389    o pkg/ecco: fix counting cost function contributions for obcs (code
390      by Matt M.) and diffkr for diagnostics
391    o pkg/ecco, pkg/ctrl, pkg/grdchk:
392      add cost penalty terms for initial uvel, vvel, eta controls
393      and I/O for prior error files
394    o pkg/mdsio:
395       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
396       (new argument) to check for tiled file in mdsioLocalDir : this fix the
397       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
398    o pkg/ctrl:
399     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
400       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
401       unused and superfluous variables
402     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
403    o pkg/ecco
404     - enable adjoint of Stevens OB
405    o pkg/ctrl/ecco/grdchk:
406      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
407        Fortunately, we do not have any tests for the numerous cpp-flagged
408        option of "obcs as control parameters" so we will never know
409        if this is an improvement (but at least now things compile).
410      - remove an obsolete initialization from ecco_cost_init_barfiles.F
411      - fix some problems within never used ifdefs to make the code compile
412    o pkg/obcs:
413     - Refine Interior mask definition to work with more complex OB (e.g.
414       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
415       read in Interior mask from file. Check if Interior mask is consistent
416       with OB list of indices.
417    o pkg/seaice
418     - beginning code for a seaice tracer package,
419       but currently only used for seaice age: SEAICE_AGE
420       SEAICE_num = 4
421       iTracer = 1: area-weighted ice age
422               = 2: volume-weighted ice age
423               = 3, 4: template for one-year vs. multi-year ice
424       data.seaice has new namelist SEAICE_PARM03 for arrays related to
425       SEAICE_num
426    
427    checkpoint62t (2011/03/05)
428    o pkg/obcs:
429     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
430       then normal component. This ensures that the normal component is set
431       correctly even when it conficts with tangential setting from an other OB.
432       Affects results of test-experiment seaice_obcs: update the output.txt
433    o pkg/obcs:
434     - add code to monitor statistics of dynamical fields at OB.
435     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
436       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
437       - change default: balance the Net inflow through all OB (instead of balancing
438         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
439     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
440       to match Nortern OB inflow (OBCS_balanceFacN=0).
441    o pkg/seaice:
442     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
443    o pkg/seaice (seaice_growth v 1.113):
444     - reverting seaice_growth to v 1.111 in order to have code with exact bit
445       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
446       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
447       runtime flag SEAICEareaFormula is kept but is inactive
448    o model/src:
449     - add new param to scale curvilinear grid distance and area when using
450       a different sphere radius from the grid-files.
451     - test/check multi-threads EXCH applied to local variable (cg2d_x)
452    o adjoint:
453     - enable adjoint of Stevens OB
454     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
455       (a bit delicate because of potentially modified adj. common block structure;
456       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
457    
458    checkpoint62s (2011/02/15)
459    o pkg/seaice (seaice_growth v 1.112):
460     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
461       computing the ice cover tendency from effective thickness tendencies. Include
462       Ian Fenty's formula.
463     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
464       SEAICEareaFormula.
465     - simplify notations for the various d_HEFF/d_AREA terms.
466    o pkg/gmredi:
467     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
468       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
469       add a verification test-run (front_relax.bvp) to test GM_useBVP.
470    o pkg/seaice (seaice_growth v 1.111):
471     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
472     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
473       also melt ice.
474    o pkg/seaice:
475     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
476     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
477    o pkg/cheapaml:
478     - from Nico Wienders: New version of this package.
479    o pkg/flt:
480     - add CPP options to prevent floats to re-enter the opposite side of
481       a periodic domain (default: keep periodicity)
482    o pkg/gmredi:
483     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
484       (needed for multi-dim advection).
485     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
486    o model/src:
487     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
488    o tutorial_tracer_adjsens
489     - extend to NLFS and replace maskC by hFacC
490       (change reference output accordingly)
491    
492    checkpoint62r (2011/01/24)
493    o testreport:
494     - add option -deloutp (-do) to remove output file after successful run
495     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
496       extract exact list of procs from this file ; adjust COMMAND by
497       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
498    o pkg/ecco: replace old ineffective way of penalizing deviations from
499      first guess (of obcs) with code by Matt Mazloff
500    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
501      exf/cal
502      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
503        and handle case of obcs?period == 0
504        Not affected by these changes: There is still an inconsistency in
505        the computation of start/endrec for the obcs variables for ALLOW_CAL
506        defined (see comment by Menemenlis, 7-Mar-2003)
507      - make S/R ctrl_get_gen_rec return something meaningful even if
508        ALLOW_CAL is not defined
509      - ctrl_getobcs?: simplify code so that it does not need to use
510                       S/R exf_swapfields
511    o testreport:
512       allow to test MPI with different number of processors for each experiment:
513       create file "SIZE.h.mpi" in each build dir.
514       Note: update of "-command" argument not yet implemented.
515    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
516      alleviate the need for additional 3D tapes when using
517      the non-inear free surface in the adjoint. This is done
518      by adding an 'update' of hfacc etc. to their current
519      value at the beginning of forward_step.F.
520    o pkg/seaice
521      seaice_lsr: move stress-divergence computations out of outer pseudo-
522      timestepping loop
523    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
524      up, so that the calls of the ctrl_* subroutines are really at the end
525      of the routine.
526    o pkg/gmredi:
527      allow to specify a 2-D horizontal map and a 1-D vertical profil
528      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
529    o pkg/seaice:
530      move lsr iterations from seaice_dynsolver to seaice_lsr.
531    o pkg/seaice:
532      reduce memory footprint of seaice mutldim advection tapes,
533      by using a 2D tape independent of the generic_advdiff ones,
534      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
535    
536    checkpoint62q (2010/12/29)
537    o model/src:
538      - check horizontal grid-spacing for unset or zero/negative values.
539      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
540    o pkg/flt:
541      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
542      - precision of input and output files set according to readBinaryPrec
543        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
544      - initial float position from tiled file was not converted to index space
545        (looks like a bug): fixed to make it similar to initial pos. global file.
546    o global_ocean.cs32x15:
547       change SIZE.h of AD set-up to get same tiling as with MPI.
548       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
549    o model/src:
550       add flag to control printing of domain fields (bathymetry, hFac ...) in
551       ini_mask_etc (call to plot_fieds_xy*).
552    o pkg/thsice:
553       if useEXF, some forcing fields are not valid in overlap: fixed by computing
554       over the interior only + apply EXCH at the end (like with SEAICE advection).
555    o pkg/mdsio:
556      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
557        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
558      - change barrier call for safe multi-threads access to 3-D shared buffer.
559      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
560      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
561        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
562    o pkg/flt:
563      - add fourth-order Runge-Kutta integration
564      - add basic exch2 support (only 1 facet supported so far!)
565    o pkg/mdsio+rw:
566      new S/R to read local (or tile independent) vector (read counterpart of
567       mds_writevec_loc, and front-end write_glvec_rl/rs).
568    o global_ocean.cs32x15: additional input_ad.seaice experiment
569        that uses pkg/seaice rather than pkg/thsice.
570        (using multidim advection for seaice)
571    o towards more F95 syntax for array specification in namelist:
572      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
573        of all verification experiments.
574           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
575          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
576      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
577    o global_ocean.cs32x15: additional input.seaice experiment
578        that uses pkg/seaice rather than pkg/thsice.
579    
580    checkpoint62p (2010/12/17)
581    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
582        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
583    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
584        allow for use of multim. advection in seaice adjoint.
585    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
586      - first attempt to close budgets by taking into account the freshwater
587        flux implied by the sublimation of snow and ice. So far only the
588        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
589        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
590    o eesupp/src:
591      new S/R with new option (NML_EXTENDED_F77) to change array specification
592      from F95 standard to commonly accepted extended F77 form.
593      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
594      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
595      for less tolerant f77 compiler (e.g., pgf77, g77).
596    o globalFiles:
597      commented out in parameter file "data" since it's not safe with MPI
598      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
599      in this case); no longer commented out in restart test (tst_2+2).
600    o add adTapeDir to specify a special directory where adjoint tapes are
601      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
602      and cannot be used together with mdsioLocalDir.
603    o nesting pkgs:
604      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
605      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
606      - add parameter files + utils dir + output from short run on beagle.
607    o pkg/seaice:
608        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
609    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
610      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
611    
612    checkpoint62o (2010/11/25)
613    o pkg/exf:
614      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
615    o pkg/seaice:
616      - seaice_ocean_stress: split a loop for better vectorization of the
617        adjoint code
618      - seaice_growth.F: fix bug in conservation of freshwater connected to
619        capping of heff, put contribution into d_HEFFbyNEG
620      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
621        by something more sensible (parameters that are what their name implies)
622      - change some defaults, so that by default exf-parameters are used for
623        things like rhoAir, cpAir,latent/sensible heat parameters, in order
624        to reproduce the old results, many data.seaice now contain funny values
625        for cpAir and latent heat of sublimation
626    o packages_readparms.F: move exf_readparms up in line so that
627        exf-parameters are visible for other packages (e.g. seaice)
628    o debugMode & debugLevel=2:
629      - differentiate between debugMode & debugLevel=2:
630        debugMode: controls printing of debug messages (sequence of S/R calls).
631        debugLevel: controls printing of algorithm intermediate results and stats.
632      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
633        => allows to print debug-stats without all sequence of call messages.
634      - switch control of debug print from debugLevel to debugMode in many S/R.
635    o pkg/obcs (obcs-sponge):
636        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
637        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
638    o pkg/generic_advdiff:
639      - record overlap minimum size for each advection scheme;
640      - refine criteria on overlap minimum size;
641      - check and stop (in gad_check) if overlap size is too small.
642    o pkg/obcs:
643      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
644        once, in ptracers_implicit.F)
645      - with seaice: remove test on empty file name in obcs_apply_seaice (always
646        apply OB values when tile has OB)
647    o model/src, coriolis setting:
648      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
649        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
650        files (selectCoriMap=3) with any grid.
651      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
652    o pkg/seaice/seaice_growth.F:
653        a few cosmetic changes that reduce the number of lines of code
654    o pkg/obcs: add boundary conditions following Stevens (1990)
655      - the code follows old MOM/NAOSIM code
656      - so far it is only implemented for the eastern and western boundaries
657        and NOT for pTracers
658    o pkg/rbcs:
659      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
660        beginning of the first rbcs forcing period.
661      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
662        offline package, i.e., one file per time, labeled by iteration number;
663        deltaTrbcs sets the timestep with which the data was generated;
664        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
665      - rbcsForcingCycle=0 makes forcing non-cyclic.
666      - make arithmetic safe for negative times and odd forcing periods.
667    
668    checkpoint62n (2010/11/09)
669    o pkg/seaice:
670        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
671    o pkg/obcs:
672       New S/R to copy tracer value from the OB location to narrow band region
673        (width = same as overlap) beyond the OB: preserve OB value (needed for
674        high-order scheme) which were overwritten by EXCH call if in overlap
675        region. Applied to theta, salt, ptracer and advected seaice variables.
676       With seaice: use maskInC in similar way as in gad_advection.F,
677        in seaice_advection.F and advect.F.
678       Update output of experiment seaice_obcs and change exp4 to test OBCS with
679        4th order Adv.Scheme. for pasive salt and ptracer.
680    o tools/genmake2:
681      - when looking for an optfile (not specified), only search for Fortran compiler
682        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
683      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
684        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
685      - set default for CPP to "cpp -traditional -P" (was the case without specifying
686        an optfile, but otherwise default was just "cpp".
687      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
688      - when "CC" is not set in the optfile, look for possible C compiler
689        (instead of just setting CC=cc)
690      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
691        => add a ".F" to ".o" rule for source files with no "#include" (such as
692           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
693      - move gfortran before g77 in list of possible Fortran compiler (consistent
694        with reference compiler switch from g77 to gfortran)
695    o pkg/seaice:
696      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
697        seaice_check that stops the model, when the CPP flag is used.
698      o seaice_growth.F: make capping of ice volume conserving by returning the
699        capped ice as freshwater to EmPmR. This does not change the verification
700        experiments but will change runs where the capping is acutally active
701    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
702      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
703         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
704         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
705    o tools/genmake2:
706      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
707      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
708      - clean previous genmake log files before anything else.
709      - change Makefile to remove testreport log files (*.tr_log) and genmake log
710        files only with "CLEAN" target (instead of "Clean");
711    o pkg/generic_advdiff:
712      Change OBCS in multiDim advection (gad_advection.F):
713       Use maskInC to prevent intermediate update of tracer-field in OB regions,
714       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
715       which were applying future time-step OB values.
716      This way, all explicit calculations use current-time-step OB values
717       (simpler and more consistent).
718      Affects results when set-up uses time-varying OBC and multi-dim advection;
719       update output of experiment seaice_obcs.
720    o pkg/seaice:
721      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
722       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
723         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
724      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
725       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
726       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
727    o pkg aim (2010/10/26):
728      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
729        formulation with obliquity, eccentricity, ... as run-time parameters,
730      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
731        upward shortwave radition at the surface (all-sky and clear-sky).
732    o pkg/obcs:
733      - writing sections with globalFiles=T does not work: switch to tiled-files
734        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
735      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
736      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
737    
738    checkpoint62m (2010/10/21)
739    o pkg/seaice: vectorize seaice_solve4temp.F
740      - move iterations loops outside of i/j-loops
741      - requires 2D arrays for TB and effConduct
742      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
743        modified in this routine
744      - a little bit of clean up, adjusting indentation, etc.
745      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
746        performance and '**TWO' by '**2' (because TWO is a float),
747        replaced ONE, ZERO
748    o eesupp/src:
749       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
750    o pkg/seaice/seaice_growth.F
751      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
752      merging process. The merged routine has two branches, and one activates the 'evolution'
753      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
754      In summary, here is what the '10/10 revision' did consist of
755        part 1: seaice_growth.F revisions 1.71 to 1.75
756          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
757            The emphasis here was on improving readability (e.g. by trying to use meaningful
758            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
759        part 1.5:
760          - revising the lab_sea experiment to make it a more useful (i.e. stable
761            and representative of an actual model run). This was done by generating a
762            (winter) pickup to start from, switching back the main experiment dynamic
763            solver from evp to lsr, having one of the experiments use the free drift solution.
764        part 2: seaice_growth.F revisions 1.76 to 1.85
765          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
766          - Sorting out the various fields units and sign (set early on and reset at the end)
767            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
768            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
769          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
770            and simplifying logical expressions to further improve readibility.
771        part 3: seaice_growth.F revisions 1.86 to 1.89
772          - Re-organize the blocks of code more logically.
773          - Merging the '_if.F' pieces that add something new.
774    o pkg/thsice:
775      - vectorize thsice_solve4temp and thsice_get_exf.
776        Problem: thsice_solve4temp has an unvectorizable statement that
777        might also be problematic for TAF
778      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
779        does not change the verifcation experiment, but will change all
780        experiments that have this flag undefined (not tested in verification);
781        a little reorganization to save a few 2D fields and recomputations
782      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
783      - 2nd step:  fix some store dirs
784        o seems to work somewhat, i.e. using ifort but not g77
785        o likely cause are incomplete init. or recomputation
786        o start verification/global_ocean.cs32x15/input_ad.thsice
787    o pkg/obcs: add support for exch2
788      - the position of the boundary and prescribed values are specified using
789        a global domain with exch2 facets stacked
790        - in x for N,S boundaries (like W2_mapIO=-1)
791        - in y for E,W boundaries (so E,W boundaries do not overlap)
792    o pkg/mdsio: add support for writing global sections with exch2
793        file layout is as for obcs described above:
794        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
795        - for y-z sections, facets are stacked in y
796    o pkg/thsice:
797       - change a few routines for better vectorization: thsice_albedo.F,
798         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
799         not affected, but in particular the latter routine has changed
800         dramatically (not necessarily easier to read now).
801       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
802       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
803    o verification/lab_sea:
804      - overhaul of the forward model experiments. The main motivation
805        for this revision is that lab_sea has proven quite fragile (when
806        changing the sea-ice code, and switching platforms) to a point
807        when failures were very hard to attribute to specific code problems.
808      - the suspected reason for this fragility is noise amplification by evp so,
809        to start with, we decided to replace evp with lsr in the main experiment.
810      - the input.lsr experiment thus became obsolete and was removed.
811      - it was replaced with the input.fd experiment that uses an
812        analytical "free drift" solution as the ice velocity field.
813      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
814        will hopefully allow us to discriminate problems due to dynamic solvers
815        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
816        us to test additional options, along with the salt plume package.
817      - Finally a pickup was generated (at the end of a one year run) to
818        make the tests more representative of an actual model run. Previously
819        the tests starting point was a 1m thickness of ice everywhere.
820    o pkg/seaice:
821      - introducing S\R seaice_freedrift.F that compute the
822        analytical solution to an approximate ice momentum
823        equation (i.e. the simple stress/coriolis balance).
824      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
825        of the free drift velocity field, and enable its use.
826        To actually use the free drift solution as the model ice
827        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
828    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
829    
830    checkpoint62l (2010/10/04)
831    o pkg/seaice:
832      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
833      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
834       version (with USE_ORIGINAL_SBI undef);
835  o add hooks for new packages OASIS, the package will follow  o add hooks for new packages OASIS, the package will follow
836    (hooks exclude the seaice pkg for now)    (hooks exclude the seaice pkg for now)
837  o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO  o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
838    Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,    Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
839    rather than mdsio_readvector.F/mdsio_writevector.F, within    rather than mdsio_readvector.F/mdsio_writevector.F, within
840    adread_adwrite.F to read/write adjoint-related tapes to disk.    adread_adwrite.F to read/write adjoint-related tapes to disk.
841  o eesup and pkg/mdsio: ALLOW_WHIO  o eesupp and pkg/mdsio: ALLOW_WHIO
842      Option to write/read 2D fields to files including tiles halos.
843    Option to write/read 2D fields to files including tiles halos.    The main purpose is for adjoint related "tape I/O".
   The main purpose is for adjoint related "tape I/O".  
844    The secondary purpose is for debugging phases.    The secondary purpose is for debugging phases.
   
845    A word on those rather specifically intended purposes.    A word on those rather specifically intended purposes.
846    The code was meant to be stripped down to the bare minimum.    The code was meant to be stripped down to the bare minimum.
847    Typically, there is a unique and basic mapping to the global    Typically, there is a unique and basic mapping to the global
848    buffer (tile by tile, then proc by proc, then level by level), and    buffer (tile by tile, then proc by proc, then level by level), and
849    byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not    byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
850    meant to generate user friendly outputs of various shapes and forms.    meant to generate user friendly outputs of various shapes and forms.
851    Rather it is intended, for the knowledgeabale developers,    Rather it is intended, for the knowledgeabale developers,
852    to be largely independent of the many mdsio options, to allow    to be largely independent of the many mdsio options, to allow
853    outputs of tiles+halos in debugging phases and in adjoint runs,    outputs of tiles+halos in debugging phases and in adjoint runs,
854    and to allow some flexibility in tuning (adoint) I/O depending on each    and to allow some flexibility in tuning (adoint) I/O depending on each
855    file system behavior. With regard to tuning, most of the potential knobs    file system behavior. With regard to tuning, most of the potential knobs
856    (to leave files open, to allocate the I/O indep. of usesinglecpuio,    (to leave files open, to allocate the I/O indep. of usesinglecpuio,
857    to specify directories, to specify the typical size of I/O calls, etc.)    to specify directories, to specify the typical size of I/O calls, etc.)
858    are not yet included, and will be added if they prove useful.    are not yet included, and will be added if they prove useful.
# Line 319  o tools/build_options: Line 1145  o tools/build_options:
1145      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1146  o pkg/ecco  o pkg/ecco
1147    - allow user defined cost function contributions    - allow user defined cost function contributions
1148          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1149          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1150    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1151        the two options are complementary.        the two options are complementary.
1152  o pkg/smooth  o pkg/smooth
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