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revision 1.1840 by jmc, Sat Mar 9 22:09:26 2013 UTC revision 1.1908 by jmc, Fri Aug 9 14:14:05 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 switch to TAF version-2:
8      - add flow directives to "freeze" naming convention for ad-routines that
9        are used in I/O routines of adjoint state and associated common blocks
10        that are used in adcommon.h (backward compatible with version-1)
11      - update all ad-optfiles (in tools/adjoint_options + few local to some
12        verification exp) to switch to latest TAF version (currently 2.5.5);
13        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
14        out except for diva).
15      - the major change with TAF version-2 is that both the differentiated
16        routines and the forward routines (new) are returned as part of the TAF
17        output source code. Update genmake2 accordingly.
18      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
19        with version-2 when compared to TLM or FWD gradient); other experiments
20        output show minor changes (machine truncation level); update the few AD &
21        TLM output with 12 matching digits only (some prior to version-2 switch).
22    
23    checkpoint64l (2013/08/05)
24    o model/src:
25      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
26      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
27        when using TAF but only if using OpenAD.
28    o pkg/mom_common+fluxform+vecinv:
29      - always set horiz. viscosity arrays to background value before calling
30        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
31        only when using variable horiz. viscosity (useVariableVisc=T);
32      - simplify mom_vecinv.F (only 1 block for momViscosity).
33    o pkg/mom_common: variable horiz. viscosity in NH code
34      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
35        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
36      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
37        useBiharmonicVisc & useVariableVisc.
38      - fix old bug (already in 1rst implementation of variable horizontal viscosity
39        in calc_gw.F, version 1.27, 2006/06/20):
40        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
41        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
42      - change background horiz viscosity in vertical momentum (gW) to always be
43        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
44        any type of variable viscosity, e.g., viscAh/4Grid)
45      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
46        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
47        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
48        default viscAh,viscA4 is zero).
49    o model/src:
50      - extend length of drC & recip_drC from Nr to Nr+1.
51    o Divided Adjoint (DIVA) with MPI:
52      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
53      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
54        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
55    
56    checkpoint64k (2013/07/23)
57    o tools/OAD_support:
58      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
59        and remove it from genmake2.
60    o tools/build_options:
61      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
62        MPI_HEADER_FILES list (let genmake2 find the missing headers)
63    o verification/halfpipe_streamice:
64      - change to driving stress formulation; update both Fwd & AD output.
65    o tools/genmake2 and Divided Adjoint with MPI:
66      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
67      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
68      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
69        Makefile, which is set by genmake2, and check which mpi-headers are needed.
70        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
71      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
72    o testreport:
73      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
74        perform additional runs (number of additional runs is "add_DIVA_runs" taken
75        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
76    o verification/lab_sea (AD test):
77      - change to test Divided Adjoint Run in this set-up (both standard AD test
78        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
79    o pkg atm_ & ocn_compon_interf:
80      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
81        staggerTimeStep implementation) and disable (retired) corresponding
82        parameter.
83    o pkg/offline:
84      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
85      - add S/R OFFLINE_CHECK to print offline parameter summary
86        and stop if loading a file that is not used;
87      - enable to calculate GMRedi tensor, KPP mixing and convective index
88        when the corresponding file(s) is/are not specified (but pkg is used).
89      - comment out resetting of monitorFreq (to endTime) since it still useful
90        for monitoring CFL numbers and checking offline fields.
91    o OpenAD:
92      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
93        smaller standard output) and generate new (smaller) output (on baudelaire
94        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
95    o model/src:
96      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
97        (where external_forcing_adjust was called) and change list of arguments;
98      - merge external_forcing_adjust.F into external_forcing_surf.F
99      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
100        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
101        previously in file "balance_relax.F", now removed); remove corresponding
102        arrays in FFIELDS.h.
103      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
104        a hack for getting back surfaceForcingS (loaded from file) when using
105        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
106      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
107        (was getting only 11 digits for AD-grad, due to different truncation
108         error in AD code).
109    
110    checkpoint64j (2013/07/04)
111    o pkg/offline:
112      - to enable the use of other features with pkg offline (e.g., obcs),
113        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
114      - comment out "allowFreezing" (now active) in 2 offline testing exp.
115    o pkg/exf ALLOW_RUNOFTEMP
116      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
117      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
118      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
119    o pkg/atm_phys:
120      - allows to add some damping on uVel,vVel (strength only function of k).
121    o verification, ad-tests:
122      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
123        global_ocean_ebm and offline_exf_seaice.thsice.
124    o verification/halfpipe_streamice:
125      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
126        flux input boundary conditions to be ignored; a fix for this bug changed
127        verification results for forward test.
128      - add adjoint test.
129    o pkg/ptracers:
130      - allow to restart without SOM pickup (resetting SOM to zero).
131    o pkg/gmredi:
132      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
133      - It uses mixing length theory and suppression by steering level effects to
134        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
135        to JPO, for more details).
136      - It also uses the diffusivity to calculate an eddy induced streamfunction
137        based on a PV closure (rather than a buoyancy closure as in GM).
138      - New files added to pkg/gmredi:
139        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
140          induced overturning streamfunction (called from gmredi_calc_tensor)
141        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
142          for use in gmredi_k3d
143        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
144          the eddy diffusivity
145    
146    checkpoint64i (2013/06/18)
147    o pkg/cheapaml:
148      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
149        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
150        with pkg/cheapaml.
151    o utils/python: add subpackage for cubed sphere function, first example is
152        simple cs.pcol to plot 2D fields on a map
153    o pkg/streamice:
154      - This is a new package in MITgcm, which solves dynamic equations for ice
155         sheets and ice streams
156      - At the moment it is independent of atmosphere/ocean dynamics, or any
157        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
158        ed that this will change)
159      - There is a new verification exercise that tests it, halfpipe_streamice,
160        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
161        rectangular embayment
162      - halfpipe_streamice is forward-only for now, will have TAF test soon
163      - for questions, email dgoldber@mit.edu
164    o pkg/thsice:
165      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
166        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
167      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
168         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
169      - allow precip from pkg/cheapaml to make snow over seaice.
170    o pkg/cfc:
171      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
172      - remove atmos CFC 2-D arrays from common bloc (now local variables)
173      - change some hard-coded constant to run time parameter for reading and
174        and interpolating atmospheric CFC ; keep same default as previously.
175      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
176      - put arguments in standard order: myTime, myIter, myThid
177      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
178        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
179      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
180      - new routine to print summary of CFC params and check for consistency.
181    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
182      similar to thsice_advdiff.
183      Note that for the B-grid case the routine parameters uc/vc are overwritten.
184    o pkg/cfc:
185      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
186        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
187      - fix interpolation of atmphspheric CFC between Sorthern and Northern
188        hemisphere value.
189    o pkg/seaice:
190      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
191    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
192                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
193      - requires an additional time level that is stored in the pickup
194      - you can start with AB2 from a pickup without this time level with
195        pickupStrictlyMatch = .false.
196    
197    checkpoint64h (2013/05/26)
198    o pkg/cheapaml:
199      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
200        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
201      - consistent treatment of uWind,vWind location: assume everywhere in
202        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
203        (Note: was already the case for Tair,Qair advection);
204        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
205      - compute diabatic forcing only in the interior (excluding overlap regions)
206      - fill in array "Qsw" (for short-wave heating);
207      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
208        before any update (consistent with MITgcm state var diagnostics);
209      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
210        non periodic ; + adjusted for uWind,vWind (C-grid).
211    o pkg/seaice:
212      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
213        add explicitly pkg/exf in experiments that currently use pkg/seaice.
214      - allows to compile pkg/seaice without pkg/exf.
215    o tools/OAD_support:
216      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
217        of array "ourStepOf" in function rvNextAction (revolve.F90).
218    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
219      - change pkg name (to be used with other atmospheric physics pkg)
220        but by-pass CVS when making the new pkg so that we keep the CVS history.
221    o pkg/offline:
222      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
223        (previously called from pkg/dic_surfforcing_init.F)
224    o model/src:
225      - re-order sequence of calls within packages_init_variables.F, using
226        standard order, except for:
227         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
228         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
229    o new pkg: atm_phys
230      - add entry point and source code (previously in contrib
231          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
232        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
233      - re-order sequence of calls within packages_readparms.F,
234         packages_init_fixed.F and packages_write_pickup.F
235        (but skip packages_init_variables.F because of TAF issues).
236      - update contrib/*/atm_gray/ experiment.
237    o pkg/seaice (ITD code):
238      - simplify and fix the writing of pickup-files for ITD case
239    o pkg/seaice (ITD code):
240      - introduce floe size dependent lateral melt for ITD case;
241      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
242      - update seaice_itd experiment main output.
243    o pkg/thsice:
244      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
245        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
246        changed accordingly pkg/atm2d.
247    
248    checkpoint64g (2013/05/01)
249    o pkg/exf ALLOW_RUNOFTEMP
250      - if defined,  river and glacier runoff temperature can be read-in from
251        runoftempfile; runoftempfile needs to have same format as runofffile
252    o pkg/thsice (& pkg/bulk_force):
253      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
254        for energy content of Precip + RunOff & Evap (like with pkg/exf).
255      - change computation domain to always be the interior (without overlap).
256      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
257    o verification/tutorial_global_oce_biogeo:
258      - add preliminary OpenAD setup (still has problems)
259    o pkg/seaice:
260      - turn some parameters for choosing the convergence criterion of
261        the inexact Newton method (JFNK) into runtime parameters for convenience
262      - clean up seaice_calc_viscosities.F: remove/retire two options for
263        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
264        the results of lab_sea/input because a division has been replaced by
265        a multiplication with the reciprocal (sumNorm)
266      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
267        convergence of solver (changes results, of course), and to test some
268        new features
269    o model/src:
270      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
271      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
272      - move forcing adjustment (balancing surface forcing) in specific S/R
273        where might also be applied exchanges (if needed) to forcing arrays.
274    o pkg/shelfice:
275      - allow to specify the Ice-Shelf mass per unit area (instead of
276        shelficeLoadAnomaly) and do the conversion from one to the other
277      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
278        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
279        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
280        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
281      - update isomip experiment forward output (get machine truncation error
282        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
283    o verification/offline_exf_seaice:
284      revise data.seaice in input.thermo and input_ad and update results accordingly
285        HO = 0.2, SEAICE_areaLossFormula = 2,
286        SEAICE_growMeltByConv = .TRUE.,
287        SEAICE_doOpenWaterMelt = .TRUE.,
288      Improve consistency with input.thsice and fix the spurious 500m ice corners
289    o verification/global_ocean.cs32x15:
290      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
291        in icedyn (thsice+seaice-dyn) test and update output.
292    o verification/offline_exf_seaice:
293      - adjust list of tested variables (with testreport) and update
294        standard test output with better slection of monitored fields.
295    o pkg/cd_code:
296      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
297        experiment lab_sea.hb87
298    o tools/genmake2:
299      - change default makedepend from the system default to tools/xmakedepend:
300        When no makedepend is specified, select tools/xmakedepend it the test pass,
301        otherwise select the system default (if exist and pass the test) or
302        try to build cyrus-makedepend ; stop if none of the 3 works.
303    o pkg/exf & pkg/thsice:
304      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
305        for energy content of Precip + RunOff & Evap. Assumes:
306       1) Rain has same temp as Air.
307       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
308       3) Run-Off comes at the temp of surface water (with same Cp)
309       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
310        put directly into Latent Heat flux & should use water-vapor heat capacity.
311       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
312        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
313    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
314        (compile when SEAICE_ALLOW_JFNK is defined)
315    o pkg/thsice:
316      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
317        implementation): move THSICE_AVE call after the advection (called directly
318        from thsice_do_advect.F).
319    o verification/global_ocean.90x40x15 and OpenAD:
320      New experiment for OpenAD is identical to the one in input_ad except that
321        multiDimAdvection=.FALSE.,
322      There is still an issue with this.
323    o pkg/thsice:
324      - account for ice velocity (ocean relative velocity) in turbulent heat flux
325        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
326        and offline_exf_seaice (main test).
327    
328    checkpoint64f (2013/03/31)
329    o verification/OpenAD:
330      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
331    o verification/isomip, pkg/shelfice and OpenAD:
332      - add OpenAD setup to this exp and make shelfice package work with OpenAD
333    o verification/tutorial_global_oce_biogeo:
334      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
335    o verification/offline_exf_seaice:
336      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
337    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
338      - add OpenAD setup to this exp and make ptracers package work with OpenAD
339    o pkg/seaice/seaice_evp.F:
340       mask the asymmetric contribution of the ice-ocean stress (when
341       the turningAngle is non-zero) over open water to avoid stripes
342       in the EVP-solutions after many EVP-substeps. This does not change
343       the verification experiment (because turningAngle=0 in that experiment),
344       but will affect other EVP solutions with turningAngle.ne.0
345  o verification, AD & TLM output:  o verification, AD & TLM output:
346    - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple    - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
347      additions and multiplications which affect results at machine truncation      additions and multiplications which affect results at machine truncation

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