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revision 1.1835 by jmc, Sat Mar 2 02:41:35 2013 UTC revision 1.1897 by jmc, Sat Jul 20 00:04:02 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 testreport:
8      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
9        perform additional runs (number of additional runs is "add_DIVA_runs" taken
10        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
11    o verification/lab_sea (AD test):
12      - change to test Divided Adjoint Run in this set-up (both standard AD test
13        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
14    o pkg atm_ & ocn_compon_interf:
15      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
16        staggerTimeStep implementation) and disable (retired) corresponding
17        parameter.
18    o pkg/offline:
19      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
20      - add S/R OFFLINE_CHECK to print offline parameter summary
21        and stop if loading a file that is not used;
22      - enable to calculate GMRedi tensor, KPP mixing and convective index
23        when the corresponding file(s) is/are not specified (but pkg is used).
24      - comment out resetting of monitorFreq (to endTime) since it still useful
25        for monitoring CFL numbers and checking offline fields.
26    o OpenAD:
27      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
28        smaller standard output) and generate new (smaller) output (on baudelaire
29        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
30    o model/src:
31      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
32        (where external_forcing_adjust was called) and change list of arguments;
33      - merge external_forcing_adjust.F into external_forcing_surf.F
34      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
35        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
36        previously in file "balance_relax.F", now removed); remove corresponding
37        arrays in FFIELDS.h.
38      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
39        a hack for getting back surfaceForcingS (loaded from file) when using
40        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
41      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
42        (was getting only 11 digits for AD-grad, due to different truncation
43         error in AD code).
44    
45    checkpoint64j (2013/07/04)
46    o pkg/offline:
47      - to enable the use of other features with pkg offline (e.g., obcs),
48        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
49      - comment out "allowFreezing" (now active) in 2 offline testing exp.
50    o pkg/exf ALLOW_RUNOFTEMP
51      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
52      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
53      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
54    o pkg/atm_phys:
55      - allows to add some damping on uVel,vVel (strength only function of k).
56    o verification, ad-tests:
57      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
58        global_ocean_ebm and offline_exf_seaice.thsice.
59    o verification/halfpipe_streamice:
60      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
61        flux input boundary conditions to be ignored; a fix for this bug changed
62        verification results for forward test.
63      - add adjoint test.
64    o pkg/ptracers:
65      - allow to restart without SOM pickup (resetting SOM to zero).
66    o pkg/gmredi:
67      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
68      - It uses mixing length theory and suppression by steering level effects to
69        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
70        to JPO, for more details).
71      - It also uses the diffusivity to calculate an eddy induced streamfunction
72        based on a PV closure (rather than a buoyancy closure as in GM).
73      - New files added to pkg/gmredi:
74        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
75          induced overturning streamfunction (called from gmredi_calc_tensor)
76        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
77          for use in gmredi_k3d
78        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
79          the eddy diffusivity
80    
81    checkpoint64i (2013/06/18)
82    o pkg/cheapaml:
83      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
84        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
85        with pkg/cheapaml.
86    o utils/python: add subpackage for cubed sphere function, first example is
87        simple cs.pcol to plot 2D fields on a map
88    o pkg/streamice:
89      - This is a new package in MITgcm, which solves dynamic equations for ice
90         sheets and ice streams
91      - At the moment it is independent of atmosphere/ocean dynamics, or any
92        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
93        ed that this will change)
94      - There is a new verification exercise that tests it, halfpipe_streamice,
95        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
96        rectangular embayment
97      - halfpipe_streamice is forward-only for now, will have TAF test soon
98      - for questions, email dgoldber@mit.edu
99    o pkg/thsice:
100      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
101        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
102      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
103         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
104      - allow precip from pkg/cheapaml to make snow over seaice.
105    o pkg/cfc:
106      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
107      - remove atmos CFC 2-D arrays from common bloc (now local variables)
108      - change some hard-coded constant to run time parameter for reading and
109        and interpolating atmospheric CFC ; keep same default as previously.
110      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
111      - put arguments in standard order: myTime, myIter, myThid
112      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
113        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
114      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
115      - new routine to print summary of CFC params and check for consistency.
116    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
117      similar to thsice_advdiff.
118      Note that for the B-grid case the routine parameters uc/vc are overwritten.
119    o pkg/cfc:
120      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
121        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
122      - fix interpolation of atmphspheric CFC between Sorthern and Northern
123        hemisphere value.
124    o pkg/seaice:
125      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
126    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
127                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
128      - requires an additional time level that is stored in the pickup
129      - you can start with AB2 from a pickup without this time level with
130        pickupStrictlyMatch = .false.
131    
132    checkpoint64h (2013/05/26)
133    o pkg/cheapaml:
134      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
135        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
136      - consistent treatment of uWind,vWind location: assume everywhere in
137        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
138        (Note: was already the case for Tair,Qair advection);
139        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
140      - compute diabatic forcing only in the interior (excluding overlap regions)
141      - fill in array "Qsw" (for short-wave heating);
142      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
143        before any update (consistent with MITgcm state var diagnostics);
144      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
145        non periodic ; + adjusted for uWind,vWind (C-grid).
146    o pkg/seaice:
147      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
148        add explicitly pkg/exf in experiments that currently use pkg/seaice.
149      - allows to compile pkg/seaice without pkg/exf.
150    o tools/OAD_support:
151      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
152        of array "ourStepOf" in function rvNextAction (revolve.F90).
153    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
154      - change pkg name (to be used with other atmospheric physics pkg)
155        but by-pass CVS when making the new pkg so that we keep the CVS history.
156    o pkg/offline:
157      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
158        (previously called from pkg/dic_surfforcing_init.F)
159    o model/src:
160      - re-order sequence of calls within packages_init_variables.F, using
161        standard order, except for:
162         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
163         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
164    o new pkg: atm_phys
165      - add entry point and source code (previously in contrib
166          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
167        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
168      - re-order sequence of calls within packages_readparms.F,
169         packages_init_fixed.F and packages_write_pickup.F
170        (but skip packages_init_variables.F because of TAF issues).
171      - update contrib/*/atm_gray/ experiment.
172    o pkg/seaice (ITD code):
173      - simplify and fix the writing of pickup-files for ITD case
174    o pkg/seaice (ITD code):
175      - introduce floe size dependent lateral melt for ITD case;
176      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
177      - update seaice_itd experiment main output.
178    o pkg/thsice:
179      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
180        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
181        changed accordingly pkg/atm2d.
182    
183    checkpoint64g (2013/05/01)
184    o pkg/exf ALLOW_RUNOFTEMP
185      - if defined,  river and glacier runoff temperature can be read-in from
186        runoftempfile; runoftempfile needs to have same format as runofffile
187    o pkg/thsice (& pkg/bulk_force):
188      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
189        for energy content of Precip + RunOff & Evap (like with pkg/exf).
190      - change computation domain to always be the interior (without overlap).
191      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
192    o verification/tutorial_global_oce_biogeo:
193      - add preliminary OpenAD setup (still has problems)
194    o pkg/seaice:
195      - turn some parameters for choosing the convergence criterion of
196        the inexact Newton method (JFNK) into runtime parameters for convenience
197      - clean up seaice_calc_viscosities.F: remove/retire two options for
198        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
199        the results of lab_sea/input because a division has been replaced by
200        a multiplication with the reciprocal (sumNorm)
201      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
202        convergence of solver (changes results, of course), and to test some
203        new features
204    o model/src:
205      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
206      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
207      - move forcing adjustment (balancing surface forcing) in specific S/R
208        where might also be applied exchanges (if needed) to forcing arrays.
209    o pkg/shelfice:
210      - allow to specify the Ice-Shelf mass per unit area (instead of
211        shelficeLoadAnomaly) and do the conversion from one to the other
212      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
213        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
214        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
215        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
216      - update isomip experiment forward output (get machine truncation error
217        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
218    o verification/offline_exf_seaice:
219      revise data.seaice in input.thermo and input_ad and update results accordingly
220        HO = 0.2, SEAICE_areaLossFormula = 2,
221        SEAICE_growMeltByConv = .TRUE.,
222        SEAICE_doOpenWaterMelt = .TRUE.,
223      Improve consistency with input.thsice and fix the spurious 500m ice corners
224    o verification/global_ocean.cs32x15:
225      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
226        in icedyn (thsice+seaice-dyn) test and update output.
227    o verification/offline_exf_seaice:
228      - adjust list of tested variables (with testreport) and update
229        standard test output with better slection of monitored fields.
230    o pkg/cd_code:
231      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
232        experiment lab_sea.hb87
233    o tools/genmake2:
234      - change default makedepend from the system default to tools/xmakedepend:
235        When no makedepend is specified, select tools/xmakedepend it the test pass,
236        otherwise select the system default (if exist and pass the test) or
237        try to build cyrus-makedepend ; stop if none of the 3 works.
238    o pkg/exf & pkg/thsice:
239      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
240        for energy content of Precip + RunOff & Evap. Assumes:
241       1) Rain has same temp as Air.
242       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
243       3) Run-Off comes at the temp of surface water (with same Cp)
244       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
245        put directly into Latent Heat flux & should use water-vapor heat capacity.
246       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
247        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
248    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
249        (compile when SEAICE_ALLOW_JFNK is defined)
250    o pkg/thsice:
251      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
252        implementation): move THSICE_AVE call after the advection (called directly
253        from thsice_do_advect.F).
254    o verification/global_ocean.90x40x15 and OpenAD:
255      New experiment for OpenAD is identical to the one in input_ad except that
256        multiDimAdvection=.FALSE.,
257      There is still an issue with this.
258    o pkg/thsice:
259      - account for ice velocity (ocean relative velocity) in turbulent heat flux
260        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
261        and offline_exf_seaice (main test).
262    
263    checkpoint64f (2013/03/31)
264    o verification/OpenAD:
265      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
266    o verification/isomip, pkg/shelfice and OpenAD:
267      - add OpenAD setup to this exp and make shelfice package work with OpenAD
268    o verification/tutorial_global_oce_biogeo:
269      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
270    o verification/offline_exf_seaice:
271      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
272    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
273      - add OpenAD setup to this exp and make ptracers package work with OpenAD
274    o pkg/seaice/seaice_evp.F:
275       mask the asymmetric contribution of the ice-ocean stress (when
276       the turningAngle is non-zero) over open water to avoid stripes
277       in the EVP-solutions after many EVP-substeps. This does not change
278       the verification experiment (because turningAngle=0 in that experiment),
279       but will affect other EVP solutions with turningAngle.ne.0
280    o verification, AD & TLM output:
281      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
282        additions and multiplications which affect results at machine truncation
283        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
284        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
285        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
286        digits of matching.
287    o pkg/seaice:
288       modify lsr-algorithm so that it vectorizes AND converges by using a
289       "zebra" method: split vector loop into two with step size 2; this
290       solves a general convergence problem for the JFNK solver on a vector
291       computer. It has the potential to even improve convergence for
292       non-vector machines, but it does change the results so it is turned
293       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
294       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
295    
296    checkpoint64e (2013/03/05)
297    o pkg/ecco and several verification experiments:
298       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
299       from ecco package, and revert to unified routine in model/src/
300       Adjust verification experiments accordingly, especially gloal_oce_llc90
301       Should conclude long-standing work by Gael to reconsile the_main_loop with
302       ECCO and will enable OpenAD's revolve loop in ECCO setup.
303    o pkg/generic_advdiff:
304      - implement compressible flow method for multi-dim advection (similar to
305        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
306        TAF generates many recomputations) to use it; no yet coded with implicit
307        vertical advection.
308      - change experiment advect_cs (new output) and advect_xy (same output)
309        to test compressible flow multi-dim advection.
310  o pkg/generic_advdiff:  o pkg/generic_advdiff:
311    - fix SOM advection for unusual cases (linear Free-Surf in r*, other    - fix SOM advection for unusual cases (linear Free-Surf in r*, other
312      cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)      cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
# Line 23  o pkg/seaice: reorganize seaice_lsr.F to Line 326  o pkg/seaice: reorganize seaice_lsr.F to
326    - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS    - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
327    - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner    - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
328  o OpenAD support  o OpenAD support
329    Reorganize S/R call for overall time-stepping loop to facilitate     Reorganize S/R call for overall time-stepping loop to facilitate
330    OpenAD revolve loop replacement     OpenAD revolve loop replacement
331    (new S/R main_do_loop.F)     (new S/R main_do_loop.F)
332  o model/src:  o model/src:
333    - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;    - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
334    - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R    - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R

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