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revision 1.1851 by jmc, Fri Apr 5 21:29:21 2013 UTC revision 1.1915 by jmc, Thu Aug 22 01:20:58 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 tools:
8      - genmake2: define a common prefix for all temp-file names ; allow to move
9        them to local /tmp disc (but commented out for now);
10      - xmakedepend: add the same switch for temp-files (but commented out).
11    o pkg/offline:
12      - changes for usewith rStar (NLFS): assume that we continue to provide
13        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
14        output files) and apply r* scaling at each time-step (function of the time
15        varying Eta field); use normal pickup files (needed for restart with NLFS).
16    o adjoint with OpenAD:
17      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
18        package openad.  This package has to be compiled for all runs with OpenAD
19        instead of specifying code_oad_all as a modification directory.
20      - link the fortran templates from tools/OAD_support to the build directory
21        for preprocessing to avoid conflicts between different setups compiled
22        simultaneously and simplify cleanup.
23    o pkg/exf:
24      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
25        main model or other pkgs are exchanged in EXF_MAPFIELDS).
26    o model/src:
27      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
28        (similar to do_fields_blocking_exchanges.F).
29    o tools/genmake2:
30      - remove TAF output src code just before calling staf (when not doing a fresh
31        built, will stop if things go wrong with staf).
32      - fix target "adobj" (left from TAF version-2 transition)
33    o pkg/diagnostics:
34      - add a parameter to track the status of pkg/diagnostics activation;
35        this replace/extend the use of logical param "settingDiags" (to check
36        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
37        New S/R to print error message and stop when pkgStatus is not right.
38      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
39    
40    checkpoint64m (2013/08/13)
41    o model/inc:
42      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
43        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
44    o pkg/kpp & aim_v23:
45      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
46    o pkg/seaice:
47      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
48        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
49      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
50    o eesupp/src:
51      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
52        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
53    o switch to TAF version-2:
54      - add flow directives to "freeze" naming convention for ad-routines that
55        are used in I/O routines of adjoint state and associated common blocks
56        that are used in adcommon.h (backward compatible with version-1)
57      - update all ad-optfiles (in tools/adjoint_options + few local to some
58        verification exp) to switch to latest TAF version (currently 2.5.5);
59        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
60        out except for diva).
61      - the major change with TAF version-2 is that both the differentiated
62        routines and the forward routines (new) are returned as part of the TAF
63        output source code. Update genmake2 accordingly.
64      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
65        with version-2 when compared to TLM or FWD gradient); other experiments
66        output show minor changes (machine truncation level); update the few AD &
67        TLM output with 12 matching digits only (some prior to version-2 switch).
68    
69    checkpoint64l (2013/08/05)
70    o model/src:
71      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
72      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
73        when using TAF but only if using OpenAD.
74    o pkg/mom_common+fluxform+vecinv:
75      - always set horiz. viscosity arrays to background value before calling
76        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
77        only when using variable horiz. viscosity (useVariableVisc=T);
78      - simplify mom_vecinv.F (only 1 block for momViscosity).
79    o pkg/mom_common: variable horiz. viscosity in NH code
80      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
81        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
82      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
83        useBiharmonicVisc & useVariableVisc.
84      - fix old bug (already in 1rst implementation of variable horizontal viscosity
85        in calc_gw.F, version 1.27, 2006/06/20):
86        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
87        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
88      - change background horiz viscosity in vertical momentum (gW) to always be
89        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
90        any type of variable viscosity, e.g., viscAh/4Grid)
91      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
92        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
93        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
94        default viscAh,viscA4 is zero).
95    o model/src:
96      - extend length of drC & recip_drC from Nr to Nr+1.
97    o Divided Adjoint (DIVA) with MPI:
98      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
99      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
100        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
101    
102    checkpoint64k (2013/07/23)
103    o tools/OAD_support:
104      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
105        and remove it from genmake2.
106    o tools/build_options:
107      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
108        MPI_HEADER_FILES list (let genmake2 find the missing headers)
109    o verification/halfpipe_streamice:
110      - change to driving stress formulation; update both Fwd & AD output.
111    o tools/genmake2 and Divided Adjoint with MPI:
112      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
113      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
114      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
115        Makefile, which is set by genmake2, and check which mpi-headers are needed.
116        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
117      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
118    o testreport:
119      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
120        perform additional runs (number of additional runs is "add_DIVA_runs" taken
121        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
122    o verification/lab_sea (AD test):
123      - change to test Divided Adjoint Run in this set-up (both standard AD test
124        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
125    o pkg atm_ & ocn_compon_interf:
126      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
127        staggerTimeStep implementation) and disable (retired) corresponding
128        parameter.
129    o pkg/offline:
130      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
131      - add S/R OFFLINE_CHECK to print offline parameter summary
132        and stop if loading a file that is not used;
133      - enable to calculate GMRedi tensor, KPP mixing and convective index
134        when the corresponding file(s) is/are not specified (but pkg is used).
135      - comment out resetting of monitorFreq (to endTime) since it still useful
136        for monitoring CFL numbers and checking offline fields.
137    o OpenAD:
138      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
139        smaller standard output) and generate new (smaller) output (on baudelaire
140        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
141    o model/src:
142      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
143        (where external_forcing_adjust was called) and change list of arguments;
144      - merge external_forcing_adjust.F into external_forcing_surf.F
145      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
146        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
147        previously in file "balance_relax.F", now removed); remove corresponding
148        arrays in FFIELDS.h.
149      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
150        a hack for getting back surfaceForcingS (loaded from file) when using
151        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
152      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
153        (was getting only 11 digits for AD-grad, due to different truncation
154         error in AD code).
155    
156    checkpoint64j (2013/07/04)
157    o pkg/offline:
158      - to enable the use of other features with pkg offline (e.g., obcs),
159        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
160      - comment out "allowFreezing" (now active) in 2 offline testing exp.
161    o pkg/exf ALLOW_RUNOFTEMP
162      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
163      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
164      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
165    o pkg/atm_phys:
166      - allows to add some damping on uVel,vVel (strength only function of k).
167    o verification, ad-tests:
168      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
169        global_ocean_ebm and offline_exf_seaice.thsice.
170    o verification/halfpipe_streamice:
171      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
172        flux input boundary conditions to be ignored; a fix for this bug changed
173        verification results for forward test.
174      - add adjoint test.
175    o pkg/ptracers:
176      - allow to restart without SOM pickup (resetting SOM to zero).
177    o pkg/gmredi:
178      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
179      - It uses mixing length theory and suppression by steering level effects to
180        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
181        to JPO, for more details).
182      - It also uses the diffusivity to calculate an eddy induced streamfunction
183        based on a PV closure (rather than a buoyancy closure as in GM).
184      - New files added to pkg/gmredi:
185        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
186          induced overturning streamfunction (called from gmredi_calc_tensor)
187        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
188          for use in gmredi_k3d
189        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
190          the eddy diffusivity
191    
192    checkpoint64i (2013/06/18)
193    o pkg/cheapaml:
194      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
195        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
196        with pkg/cheapaml.
197    o utils/python: add subpackage for cubed sphere function, first example is
198        simple cs.pcol to plot 2D fields on a map
199    o pkg/streamice:
200      - This is a new package in MITgcm, which solves dynamic equations for ice
201         sheets and ice streams
202      - At the moment it is independent of atmosphere/ocean dynamics, or any
203        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
204        ed that this will change)
205      - There is a new verification exercise that tests it, halfpipe_streamice,
206        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
207        rectangular embayment
208      - halfpipe_streamice is forward-only for now, will have TAF test soon
209      - for questions, email dgoldber@mit.edu
210    o pkg/thsice:
211      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
212        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
213      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
214         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
215      - allow precip from pkg/cheapaml to make snow over seaice.
216    o pkg/cfc:
217      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
218      - remove atmos CFC 2-D arrays from common bloc (now local variables)
219      - change some hard-coded constant to run time parameter for reading and
220        and interpolating atmospheric CFC ; keep same default as previously.
221      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
222      - put arguments in standard order: myTime, myIter, myThid
223      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
224        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
225      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
226      - new routine to print summary of CFC params and check for consistency.
227    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
228      similar to thsice_advdiff.
229      Note that for the B-grid case the routine parameters uc/vc are overwritten.
230    o pkg/cfc:
231      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
232        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
233      - fix interpolation of atmphspheric CFC between Sorthern and Northern
234        hemisphere value.
235    o pkg/seaice:
236      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
237    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
238                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
239      - requires an additional time level that is stored in the pickup
240      - you can start with AB2 from a pickup without this time level with
241        pickupStrictlyMatch = .false.
242    
243    checkpoint64h (2013/05/26)
244    o pkg/cheapaml:
245      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
246        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
247      - consistent treatment of uWind,vWind location: assume everywhere in
248        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
249        (Note: was already the case for Tair,Qair advection);
250        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
251      - compute diabatic forcing only in the interior (excluding overlap regions)
252      - fill in array "Qsw" (for short-wave heating);
253      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
254        before any update (consistent with MITgcm state var diagnostics);
255      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
256        non periodic ; + adjusted for uWind,vWind (C-grid).
257    o pkg/seaice:
258      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
259        add explicitly pkg/exf in experiments that currently use pkg/seaice.
260      - allows to compile pkg/seaice without pkg/exf.
261    o tools/OAD_support:
262      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
263        of array "ourStepOf" in function rvNextAction (revolve.F90).
264    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
265      - change pkg name (to be used with other atmospheric physics pkg)
266        but by-pass CVS when making the new pkg so that we keep the CVS history.
267    o pkg/offline:
268      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
269        (previously called from pkg/dic_surfforcing_init.F)
270    o model/src:
271      - re-order sequence of calls within packages_init_variables.F, using
272        standard order, except for:
273         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
274         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
275    o new pkg: atm_phys
276      - add entry point and source code (previously in contrib
277          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
278        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
279      - re-order sequence of calls within packages_readparms.F,
280         packages_init_fixed.F and packages_write_pickup.F
281        (but skip packages_init_variables.F because of TAF issues).
282      - update contrib/*/atm_gray/ experiment.
283    o pkg/seaice (ITD code):
284      - simplify and fix the writing of pickup-files for ITD case
285    o pkg/seaice (ITD code):
286      - introduce floe size dependent lateral melt for ITD case;
287      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
288      - update seaice_itd experiment main output.
289    o pkg/thsice:
290      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
291        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
292        changed accordingly pkg/atm2d.
293    
294    checkpoint64g (2013/05/01)
295    o pkg/exf ALLOW_RUNOFTEMP
296      - if defined,  river and glacier runoff temperature can be read-in from
297        runoftempfile; runoftempfile needs to have same format as runofffile
298    o pkg/thsice (& pkg/bulk_force):
299      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
300        for energy content of Precip + RunOff & Evap (like with pkg/exf).
301      - change computation domain to always be the interior (without overlap).
302      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
303    o verification/tutorial_global_oce_biogeo:
304      - add preliminary OpenAD setup (still has problems)
305    o pkg/seaice:
306      - turn some parameters for choosing the convergence criterion of
307        the inexact Newton method (JFNK) into runtime parameters for convenience
308      - clean up seaice_calc_viscosities.F: remove/retire two options for
309        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
310        the results of lab_sea/input because a division has been replaced by
311        a multiplication with the reciprocal (sumNorm)
312      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
313        convergence of solver (changes results, of course), and to test some
314        new features
315    o model/src:
316      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
317      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
318      - move forcing adjustment (balancing surface forcing) in specific S/R
319        where might also be applied exchanges (if needed) to forcing arrays.
320    o pkg/shelfice:
321      - allow to specify the Ice-Shelf mass per unit area (instead of
322        shelficeLoadAnomaly) and do the conversion from one to the other
323      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
324        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
325        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
326        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
327      - update isomip experiment forward output (get machine truncation error
328        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
329    o verification/offline_exf_seaice:
330      revise data.seaice in input.thermo and input_ad and update results accordingly
331        HO = 0.2, SEAICE_areaLossFormula = 2,
332        SEAICE_growMeltByConv = .TRUE.,
333        SEAICE_doOpenWaterMelt = .TRUE.,
334      Improve consistency with input.thsice and fix the spurious 500m ice corners
335    o verification/global_ocean.cs32x15:
336      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
337        in icedyn (thsice+seaice-dyn) test and update output.
338    o verification/offline_exf_seaice:
339      - adjust list of tested variables (with testreport) and update
340        standard test output with better slection of monitored fields.
341    o pkg/cd_code:
342      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
343        experiment lab_sea.hb87
344  o tools/genmake2:  o tools/genmake2:
345    - change default makedepend from the system default to tools/xmakedepend:    - change default makedepend from the system default to tools/xmakedepend:
346      When no makedepend is specified, select tools/xmakedepend it the test pass,      When no makedepend is specified, select tools/xmakedepend it the test pass,

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