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revision 1.1783 by mlosch, Mon Dec 17 15:38:59 2012 UTC revision 1.1906 by jmc, Sat Aug 3 23:16:19 2013 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o model/src:
8      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
9      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
10        when using TAF but only if using OpenAD.
11    o pkg/mom_common+fluxform+vecinv:
12      - always set horiz. viscosity arrays to background value before calling
13        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
14        only when using variable horiz. viscosity (useVariableVisc=T);
15      - simplify mom_vecinv.F (only 1 block for momViscosity).
16    o pkg/mom_common: variable horiz. viscosity in NH code
17      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
18        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
19      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
20        useBiharmonicVisc & useVariableVisc.
21      - fix old bug (already in 1rst implementation of variable horizontal viscosity
22        in calc_gw.F, version 1.27, 2006/06/20):
23        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
24        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
25      - change background horiz viscosity in vertical momentum (gW) to always be
26        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
27        any type of variable viscosity, e.g., viscAh/4Grid)
28      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
29        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
30        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
31        default viscAh,viscA4 is zero).
32    o model/src:
33      - extend length of drC & recip_drC from Nr to Nr+1.
34    o Divided Adjoint (DIVA) with MPI:
35      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
36      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
37        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
38    
39    checkpoint64k (2013/07/23)
40    o tools/OAD_support:
41      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
42        and remove it from genmake2.
43    o tools/build_options:
44      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
45        MPI_HEADER_FILES list (let genmake2 find the missing headers)
46    o verification/halfpipe_streamice:
47      - change to driving stress formulation; update both Fwd & AD output.
48    o tools/genmake2 and Divided Adjoint with MPI:
49      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
50      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
51      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
52        Makefile, which is set by genmake2, and check which mpi-headers are needed.
53        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
54      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
55    o testreport:
56      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
57        perform additional runs (number of additional runs is "add_DIVA_runs" taken
58        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
59    o verification/lab_sea (AD test):
60      - change to test Divided Adjoint Run in this set-up (both standard AD test
61        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
62    o pkg atm_ & ocn_compon_interf:
63      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
64        staggerTimeStep implementation) and disable (retired) corresponding
65        parameter.
66    o pkg/offline:
67      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
68      - add S/R OFFLINE_CHECK to print offline parameter summary
69        and stop if loading a file that is not used;
70      - enable to calculate GMRedi tensor, KPP mixing and convective index
71        when the corresponding file(s) is/are not specified (but pkg is used).
72      - comment out resetting of monitorFreq (to endTime) since it still useful
73        for monitoring CFL numbers and checking offline fields.
74    o OpenAD:
75      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
76        smaller standard output) and generate new (smaller) output (on baudelaire
77        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
78    o model/src:
79      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
80        (where external_forcing_adjust was called) and change list of arguments;
81      - merge external_forcing_adjust.F into external_forcing_surf.F
82      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
83        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
84        previously in file "balance_relax.F", now removed); remove corresponding
85        arrays in FFIELDS.h.
86      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
87        a hack for getting back surfaceForcingS (loaded from file) when using
88        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
89      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
90        (was getting only 11 digits for AD-grad, due to different truncation
91         error in AD code).
92    
93    checkpoint64j (2013/07/04)
94    o pkg/offline:
95      - to enable the use of other features with pkg offline (e.g., obcs),
96        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
97      - comment out "allowFreezing" (now active) in 2 offline testing exp.
98    o pkg/exf ALLOW_RUNOFTEMP
99      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
100      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
101      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
102    o pkg/atm_phys:
103      - allows to add some damping on uVel,vVel (strength only function of k).
104    o verification, ad-tests:
105      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
106        global_ocean_ebm and offline_exf_seaice.thsice.
107    o verification/halfpipe_streamice:
108      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
109        flux input boundary conditions to be ignored; a fix for this bug changed
110        verification results for forward test.
111      - add adjoint test.
112    o pkg/ptracers:
113      - allow to restart without SOM pickup (resetting SOM to zero).
114    o pkg/gmredi:
115      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
116      - It uses mixing length theory and suppression by steering level effects to
117        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
118        to JPO, for more details).
119      - It also uses the diffusivity to calculate an eddy induced streamfunction
120        based on a PV closure (rather than a buoyancy closure as in GM).
121      - New files added to pkg/gmredi:
122        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
123          induced overturning streamfunction (called from gmredi_calc_tensor)
124        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
125          for use in gmredi_k3d
126        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
127          the eddy diffusivity
128    
129    checkpoint64i (2013/06/18)
130    o pkg/cheapaml:
131      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
132        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
133        with pkg/cheapaml.
134    o utils/python: add subpackage for cubed sphere function, first example is
135        simple cs.pcol to plot 2D fields on a map
136    o pkg/streamice:
137      - This is a new package in MITgcm, which solves dynamic equations for ice
138         sheets and ice streams
139      - At the moment it is independent of atmosphere/ocean dynamics, or any
140        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
141        ed that this will change)
142      - There is a new verification exercise that tests it, halfpipe_streamice,
143        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
144        rectangular embayment
145      - halfpipe_streamice is forward-only for now, will have TAF test soon
146      - for questions, email dgoldber@mit.edu
147    o pkg/thsice:
148      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
149        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
150      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
151         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
152      - allow precip from pkg/cheapaml to make snow over seaice.
153    o pkg/cfc:
154      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
155      - remove atmos CFC 2-D arrays from common bloc (now local variables)
156      - change some hard-coded constant to run time parameter for reading and
157        and interpolating atmospheric CFC ; keep same default as previously.
158      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
159      - put arguments in standard order: myTime, myIter, myThid
160      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
161        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
162      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
163      - new routine to print summary of CFC params and check for consistency.
164    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
165      similar to thsice_advdiff.
166      Note that for the B-grid case the routine parameters uc/vc are overwritten.
167    o pkg/cfc:
168      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
169        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
170      - fix interpolation of atmphspheric CFC between Sorthern and Northern
171        hemisphere value.
172    o pkg/seaice:
173      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
174    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
175                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
176      - requires an additional time level that is stored in the pickup
177      - you can start with AB2 from a pickup without this time level with
178        pickupStrictlyMatch = .false.
179    
180    checkpoint64h (2013/05/26)
181    o pkg/cheapaml:
182      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
183        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
184      - consistent treatment of uWind,vWind location: assume everywhere in
185        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
186        (Note: was already the case for Tair,Qair advection);
187        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
188      - compute diabatic forcing only in the interior (excluding overlap regions)
189      - fill in array "Qsw" (for short-wave heating);
190      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
191        before any update (consistent with MITgcm state var diagnostics);
192      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
193        non periodic ; + adjusted for uWind,vWind (C-grid).
194    o pkg/seaice:
195      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
196        add explicitly pkg/exf in experiments that currently use pkg/seaice.
197      - allows to compile pkg/seaice without pkg/exf.
198    o tools/OAD_support:
199      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
200        of array "ourStepOf" in function rvNextAction (revolve.F90).
201    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
202      - change pkg name (to be used with other atmospheric physics pkg)
203        but by-pass CVS when making the new pkg so that we keep the CVS history.
204    o pkg/offline:
205      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
206        (previously called from pkg/dic_surfforcing_init.F)
207    o model/src:
208      - re-order sequence of calls within packages_init_variables.F, using
209        standard order, except for:
210         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
211         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
212    o new pkg: atm_phys
213      - add entry point and source code (previously in contrib
214          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
215        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
216      - re-order sequence of calls within packages_readparms.F,
217         packages_init_fixed.F and packages_write_pickup.F
218        (but skip packages_init_variables.F because of TAF issues).
219      - update contrib/*/atm_gray/ experiment.
220    o pkg/seaice (ITD code):
221      - simplify and fix the writing of pickup-files for ITD case
222    o pkg/seaice (ITD code):
223      - introduce floe size dependent lateral melt for ITD case;
224      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
225      - update seaice_itd experiment main output.
226    o pkg/thsice:
227      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
228        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
229        changed accordingly pkg/atm2d.
230    
231    checkpoint64g (2013/05/01)
232    o pkg/exf ALLOW_RUNOFTEMP
233      - if defined,  river and glacier runoff temperature can be read-in from
234        runoftempfile; runoftempfile needs to have same format as runofffile
235    o pkg/thsice (& pkg/bulk_force):
236      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
237        for energy content of Precip + RunOff & Evap (like with pkg/exf).
238      - change computation domain to always be the interior (without overlap).
239      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
240    o verification/tutorial_global_oce_biogeo:
241      - add preliminary OpenAD setup (still has problems)
242    o pkg/seaice:
243      - turn some parameters for choosing the convergence criterion of
244        the inexact Newton method (JFNK) into runtime parameters for convenience
245      - clean up seaice_calc_viscosities.F: remove/retire two options for
246        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
247        the results of lab_sea/input because a division has been replaced by
248        a multiplication with the reciprocal (sumNorm)
249      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
250        convergence of solver (changes results, of course), and to test some
251        new features
252    o model/src:
253      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
254      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
255      - move forcing adjustment (balancing surface forcing) in specific S/R
256        where might also be applied exchanges (if needed) to forcing arrays.
257    o pkg/shelfice:
258      - allow to specify the Ice-Shelf mass per unit area (instead of
259        shelficeLoadAnomaly) and do the conversion from one to the other
260      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
261        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
262        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
263        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
264      - update isomip experiment forward output (get machine truncation error
265        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
266    o verification/offline_exf_seaice:
267      revise data.seaice in input.thermo and input_ad and update results accordingly
268        HO = 0.2, SEAICE_areaLossFormula = 2,
269        SEAICE_growMeltByConv = .TRUE.,
270        SEAICE_doOpenWaterMelt = .TRUE.,
271      Improve consistency with input.thsice and fix the spurious 500m ice corners
272    o verification/global_ocean.cs32x15:
273      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
274        in icedyn (thsice+seaice-dyn) test and update output.
275    o verification/offline_exf_seaice:
276      - adjust list of tested variables (with testreport) and update
277        standard test output with better slection of monitored fields.
278    o pkg/cd_code:
279      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
280        experiment lab_sea.hb87
281    o tools/genmake2:
282      - change default makedepend from the system default to tools/xmakedepend:
283        When no makedepend is specified, select tools/xmakedepend it the test pass,
284        otherwise select the system default (if exist and pass the test) or
285        try to build cyrus-makedepend ; stop if none of the 3 works.
286    o pkg/exf & pkg/thsice:
287      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
288        for energy content of Precip + RunOff & Evap. Assumes:
289       1) Rain has same temp as Air.
290       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
291       3) Run-Off comes at the temp of surface water (with same Cp)
292       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
293        put directly into Latent Heat flux & should use water-vapor heat capacity.
294       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
295        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
296    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
297        (compile when SEAICE_ALLOW_JFNK is defined)
298    o pkg/thsice:
299      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
300        implementation): move THSICE_AVE call after the advection (called directly
301        from thsice_do_advect.F).
302    o verification/global_ocean.90x40x15 and OpenAD:
303      New experiment for OpenAD is identical to the one in input_ad except that
304        multiDimAdvection=.FALSE.,
305      There is still an issue with this.
306    o pkg/thsice:
307      - account for ice velocity (ocean relative velocity) in turbulent heat flux
308        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
309        and offline_exf_seaice (main test).
310    
311    checkpoint64f (2013/03/31)
312    o verification/OpenAD:
313      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
314    o verification/isomip, pkg/shelfice and OpenAD:
315      - add OpenAD setup to this exp and make shelfice package work with OpenAD
316    o verification/tutorial_global_oce_biogeo:
317      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
318    o verification/offline_exf_seaice:
319      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
320    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
321      - add OpenAD setup to this exp and make ptracers package work with OpenAD
322    o pkg/seaice/seaice_evp.F:
323       mask the asymmetric contribution of the ice-ocean stress (when
324       the turningAngle is non-zero) over open water to avoid stripes
325       in the EVP-solutions after many EVP-substeps. This does not change
326       the verification experiment (because turningAngle=0 in that experiment),
327       but will affect other EVP solutions with turningAngle.ne.0
328    o verification, AD & TLM output:
329      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
330        additions and multiplications which affect results at machine truncation
331        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
332        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
333        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
334        digits of matching.
335    o pkg/seaice:
336       modify lsr-algorithm so that it vectorizes AND converges by using a
337       "zebra" method: split vector loop into two with step size 2; this
338       solves a general convergence problem for the JFNK solver on a vector
339       computer. It has the potential to even improve convergence for
340       non-vector machines, but it does change the results so it is turned
341       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
342       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
343    
344    checkpoint64e (2013/03/05)
345    o pkg/ecco and several verification experiments:
346       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
347       from ecco package, and revert to unified routine in model/src/
348       Adjust verification experiments accordingly, especially gloal_oce_llc90
349       Should conclude long-standing work by Gael to reconsile the_main_loop with
350       ECCO and will enable OpenAD's revolve loop in ECCO setup.
351    o pkg/generic_advdiff:
352      - implement compressible flow method for multi-dim advection (similar to
353        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
354        TAF generates many recomputations) to use it; no yet coded with implicit
355        vertical advection.
356      - change experiment advect_cs (new output) and advect_xy (same output)
357        to test compressible flow multi-dim advection.
358    o pkg/generic_advdiff:
359      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
360        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
361    o pkg/seaice:
362      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
363        bug affects two verification experiments (lab_sea and lab_sea.hb87),
364        recover old (wrong) results by setting noSlipFac = 2. in
365        seaice_calc_strainrates.F;
366      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
367      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
368        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
369      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
370    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
371      - new subroutines seaice_lsr_tridiagu/v
372      - introduce loop bounds i/jmin/max to be able to use a restricted
373        additive Schwarz method, but not used for now.
374      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
375      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
376    o OpenAD support
377       Reorganize S/R call for overall time-stepping loop to facilitate
378       OpenAD revolve loop replacement
379       (new S/R main_do_loop.F)
380    o model/src:
381      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
382      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
383        ADAMS_BASHFORTH2.
384    o pkg/cheapaml:
385      - add new parameter (default=F, same as before) to disable full domain
386        (including land) periodicity in X & Y dir.
387      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
388        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
389        into single S/R CHEAPAML_TIMESTEP.
390    
391    checkpoint64d (2013/02/17)
392    o pkg/monitor (angular momentum):
393      - do not add Eta contribution to the total AM if using rigid-lid;
394      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
395      - horizontal discretisation: compute Zonal wind contribution separately for
396        each component (instead of from cell centered averaged) and use the 4
397        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
398      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
399        FreeSurf) if using vectorInvariant momentum.
400    o model/src (horizontal grid):
401      - move initialisation of all horizontal grid arrays to null value
402        from specific horizontal grid S/R to main S/R INI_GRID;
403      - add 2 new arrays to project model C-grid velocity on to zonal direction
404        (similar to AngleCosC & -AngleSinC but at U and V point location) and
405        compute them in S/R CALC_GRID_ANGLES.
406    o pkg/seaice: replace a hard coded parameter by a runtime parameter
407        SEAICE_JFNK_tolIter
408    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
409        preconditioner for JFNK (run LSR into the overlaps as far as possible,
410        i.e OLx/y-2, but overwrite the solution in the overlaps)
411      - extend loop range in seaice_calc_viscosity
412      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
413      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
414      - slightly modify loops in tridiagonal solver lsr-preconditioner
415      - by default remove the extra exchange in seaice_preconditioner with a
416        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
417      - modify offline_exf_seaice so that old results without RAS are reproduced
418        for output.dyn_jfnk.txt
419      in seaice_fgmres.F (unrelated to RAS)
420      - add a cpp-flag option for a re-ordered mapping (potentially more
421        efficient), but because this changes the results, turn it off by
422        default
423      - replace the save statement by local common blocks
424    o utils/matlab:
425      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
426      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
427        instead of local script "load_cs.m".
428    o pkg/seaice:
429      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
430        to the scalarProductMetric and the unrolling. By chance this does not
431        change the verification experiment, because of the particular domain
432        decomposition
433    o pkg/diagnostics:
434      - change default missing_value from UNSET_RL to -999.
435    o pkg/layers: improve vectorization of layers_fluxcalc.F
436      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
437        time spent in this routine by more than a factor of 3 on an NEC-SX8
438      - step 2: replace search algorithm by a bisection algorithm found in
439        Press et al. Numerical Recipes in Fortran. This algorithm can be
440        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
441        For now, use this algorithm only for TARGET_NEC_SX defined.
442      - moved the search algorithm into a separate subroutine, that is kept
443        within the same file for automatic inlining.
444      - modified catching potential errors
445    o pkg/ecco:
446      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
447    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
448      - modifications for ALLOW_GENTIM2D_CONTROL
449      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
450      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
451      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
452      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
453    o model/src:
454      - account for moist thermodynamics in (dry) potential temperature equation;
455        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
456        and cpl_aim+ocn.
457      - also switch to standard compiler (gfortran, was using ifort previously)
458        for fizhi-cs experiments reference output.
459    o pkg/ctrl:
460      - 1st step toward generic time-varying control variable (2D) via CPP option
461        ALLOW_GENTIM2D_CONTROL
462      - note new namelist ctrl_nml_genarr in data.ctrl
463    o verification/global_ocean.cs32x15:
464      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
465        thsice calling sequence and update "output.icedyn.txt" output file.
466    o pkg/ptracers:
467      - from Ryan A.: code to allow to restart a tracer at regular time interval
468        specifying a reset frequency and a reset-phase (for each tracers).
469    o pkg/thsice:
470      - implement new sequence of calls for thsice+seaice:
471          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
472          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
473      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
474        in CPP_OPTIONS.h) to recover old sequence;
475      - update diagnostics for Intermediate State thsice diagnostics: now filled
476        just before advection (instead of just after advection in old sequence);
477      - update output of experiment offline_exf_seaice (standard test);
478      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
479        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
480    o pkg/aim_v23:
481      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
482      - use standard pkg/mdsio routines to read & write CO2 pickup file;
483      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
484      - Implement new sequence of calls for seaice advection (with thsice and
485        seaice diffusion): do ice advection after ice-Thermodynamic (previously
486        was done before); change aim_do_physics.F (split the bi,bj loops block);
487      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
488    o pkg/thsice:
489      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
490        where just seaice diffusion is used without seaice-dynamics.
491    
492    checkpoint64c (2013/01/18)
493    o pkg/seaice:
494      - add a parameter JFNKres_tFac that can replace JFNKres_t
495        (= JFNKres_tFac*JFNKresidual before JFNK solver)
496      - add a line search option to the JFNK solver
497      - move update of u/vIce and computation of initial residual into a separate
498        routine (same file); makes the code a little easier to read (?)
499      - the line search requires computation of the residual and for some reason
500        I cannot do the update of u/vIce at the beginning of the Newton loop
501        without changing the results, so we move computation of the new residual
502        also to the end of the Newton loop, even without the line search
503    o pkg/mdsio:
504      - write missing value (corresponding to undefined array value) to meta files;
505        skip this if missing value is one (UNSET_RL would be a better value for the
506        case of undefined missing value but it's current the default missing-value);
507        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
508    o pkg/exf & thsice:
509      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
510        diagnostics) even when SHORTWAVE_HEATING is #undef;
511    o verification/cfc_example:
512      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
513        illustrate how to use it).
514    o verification/offline_exf_seaice:
515      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
516        files to only one time-record.
517      in input.thermo: narrow the 2 bands of low initial ice-concentration near
518        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
519        snapshot output; same mcPheePiston value as in thsice with
520        surf-current=0.2m/s.
521      in input.thsice: similar set-up as in input.thermo (channel with same seaice
522        initial conditions).
523    o verification/cfc_example:
524      - update file "data" with more standard choice (default rotationPeriod,
525        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
526        set deltaTFreeSurf to deltaTtracer) and update the output.
527    o pkg/layers:
528      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
529      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
530    o verification/offline_exf_seaice:
531      - set all {field}period to zero for constant-in-time forcing (not tested
532        anywhere else).
533    o verification/offline_exf_seaice:
534      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
535      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
536    o model/src:
537      - implement Finite-Volume method for (hydrostatic) presure gradient
538        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
539    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
540      - In order to be compatible with the default EVP code, this requires changing
541        the EVP code around a little; and because any small change immediately
542        breaks the lab_sea.hb87 verification experiment, the reference output is
543        updated two times (each time the remaining aggrement was only 2 digits):
544        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
545        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
546        The adjoint test lab_sea.evp also needed to be updated.
547      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
548        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
549        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
550        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
551        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
552        kept obscure, because I need to test it a little more.
553    o pkg/cheapaml:
554      - fix few incorrect type (_RL/_RS) in subroutine calls.
555    o pkg/seaice:
556      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
557        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
558    o model/src:
559      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
560        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
561        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
562    o pkg/cheapaml:
563      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
564        update output of experiment cheapAML_box.
565      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
566        and set them only in one place (cheapaml_readparms.F).
567      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
568      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
569        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
570    o model/src/the_main_loop.F:
571      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
572    o pkg/seaice:
573      - remove legacy branch code.
574      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
575    o verification/*/code*/SEAICE_OPTIONS.h:
576      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
577        SEAICE_CAP_HEFF).
578    o pkg/cheapaml:
579      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
580        to load new forcing fields.
581      - add missing "_d 0" where it's needed; + some editing (improve indentation).
582      - remove switch to "-r8" compiler option (no longer needed) in verification
583        cheapAML_box, keep same output (small trucation error differences).
584    o verification/offline_exf_seaice:
585      - add thermodynamics only test.
586    o verification/cheapAML_box:
587      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
588        keep same output (same 14 digits for cg2d).
589      - switch on "-r8" compiler option (some numerical values are missing
590        the "_d 0") and update output (only 6 digits for cg2d were preserved).
591    
592    checkpoint64b (2012/12/24)
593    o pkg/cheapaml:
594      - remove un-used variables (Qnet,EmPmR) from pickup files.
595      - store tendency of advected variables into cheapaml pickup file
596        and fix the AB-2 restart.
597    o verification/offline_exf_seaice and lab_sea adjoint:
598      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
599      - switch to 4 time steps in offline, consistent with lab_sea.
600      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
601      - update results after change of experiment seaice.
602    o pkg/seaice:
603      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
604        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
605        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
606        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
607    o model/src:
608      - add run-time parameter to select CG2D solver minimum-residual solution
609        (in case of a poor convergence).
610    o pkg/seaice/seaice_lsr.F
611      - move calculation of matrix coefficients into new
612        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
613        file; the main purpose of this change is to be able to reuse the code
614        in S/R SEAICE_PRECONDITIONER
615      - modify the computation of the residual so that the mass of sea-ice
616        is not used twice; this simplifies the calculations, but since
617        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
618        not tested in testreport---this does not affect the testreport results.
619    o verification/seaice_obcs:
620      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
621        verification/lab_sea/input.salt_plume; changes results/output.txt*
622    o model/src:
623      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
624  o pkg/seaice:  o pkg/seaice:
625    - improve description of parameters in seaice_fgmres.F and start    - improve description of parameters in seaice_fgmres.F and start
626      cleaning up the code      cleaning up the code
627    - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of    - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
628      second argument      second argument
629    - add a metric based on grid cell area to SEAICE_SCALPROD; update    - add a metric based on grid cell area to SEAICE_SCALPROD; update
630      results of offline_exf_seaice.dyn_jfnk      results of offline_exf_seaice.dyn_jfnk
# Line 30  o pkg/seaice: Line 647  o pkg/seaice:
647    - add a verification experiment for JFNK in offline_exf_seaice    - add a verification experiment for JFNK in offline_exf_seaice
648  o verification:  o verification:
649    - change (for now, only fwd test) offline_exf_seaice experiment:    - change (for now, only fwd test) offline_exf_seaice experiment:
650      use a re-entrant channel with idealized costline (trapezoidal shape)      use a re-entrant channel with idealized coastline (trapezoidal shape)
651      at southern boundary to explore seaice dynamics and thermodynamics      at southern boundary to explore seaice dynamics and thermodynamics
652      with simple forcing. Main set-up has dynamics+thermo and SST relaxation;      with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
653      secondary test (input.thsice) use thermodynamics only with SST relaxation.      secondary test (input.thsice) use thermodynamics only with SST relaxation.

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