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revision 1.1828 by jmc, Mon Feb 18 22:19:51 2013 UTC revision 1.1901 by jmc, Thu Jul 25 01:12:45 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 Divided Adjoint (DIVA) with MPI:
8      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
9      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
10        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
11    
12    checkpoint64k (2013/07/23)
13    o tools/OAD_support:
14      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
15        and remove it from genmake2.
16    o tools/build_options:
17      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
18        MPI_HEADER_FILES list (let genmake2 find the missing headers)
19    o verification/halfpipe_streamice:
20      - change to driving stress formulation; update both Fwd & AD output.
21    o tools/genmake2 and Divided Adjoint with MPI:
22      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
23      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
24      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
25        Makefile, which is set by genmake2, and check which mpi-headers are needed.
26        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
27      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
28    o testreport:
29      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
30        perform additional runs (number of additional runs is "add_DIVA_runs" taken
31        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
32    o verification/lab_sea (AD test):
33      - change to test Divided Adjoint Run in this set-up (both standard AD test
34        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
35    o pkg atm_ & ocn_compon_interf:
36      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
37        staggerTimeStep implementation) and disable (retired) corresponding
38        parameter.
39    o pkg/offline:
40      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
41      - add S/R OFFLINE_CHECK to print offline parameter summary
42        and stop if loading a file that is not used;
43      - enable to calculate GMRedi tensor, KPP mixing and convective index
44        when the corresponding file(s) is/are not specified (but pkg is used).
45      - comment out resetting of monitorFreq (to endTime) since it still useful
46        for monitoring CFL numbers and checking offline fields.
47    o OpenAD:
48      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
49        smaller standard output) and generate new (smaller) output (on baudelaire
50        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
51    o model/src:
52      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
53        (where external_forcing_adjust was called) and change list of arguments;
54      - merge external_forcing_adjust.F into external_forcing_surf.F
55      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
56        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
57        previously in file "balance_relax.F", now removed); remove corresponding
58        arrays in FFIELDS.h.
59      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
60        a hack for getting back surfaceForcingS (loaded from file) when using
61        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
62      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
63        (was getting only 11 digits for AD-grad, due to different truncation
64         error in AD code).
65    
66    checkpoint64j (2013/07/04)
67    o pkg/offline:
68      - to enable the use of other features with pkg offline (e.g., obcs),
69        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
70      - comment out "allowFreezing" (now active) in 2 offline testing exp.
71    o pkg/exf ALLOW_RUNOFTEMP
72      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
73      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
74      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
75    o pkg/atm_phys:
76      - allows to add some damping on uVel,vVel (strength only function of k).
77    o verification, ad-tests:
78      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
79        global_ocean_ebm and offline_exf_seaice.thsice.
80    o verification/halfpipe_streamice:
81      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
82        flux input boundary conditions to be ignored; a fix for this bug changed
83        verification results for forward test.
84      - add adjoint test.
85    o pkg/ptracers:
86      - allow to restart without SOM pickup (resetting SOM to zero).
87    o pkg/gmredi:
88      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
89      - It uses mixing length theory and suppression by steering level effects to
90        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
91        to JPO, for more details).
92      - It also uses the diffusivity to calculate an eddy induced streamfunction
93        based on a PV closure (rather than a buoyancy closure as in GM).
94      - New files added to pkg/gmredi:
95        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
96          induced overturning streamfunction (called from gmredi_calc_tensor)
97        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
98          for use in gmredi_k3d
99        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
100          the eddy diffusivity
101    
102    checkpoint64i (2013/06/18)
103    o pkg/cheapaml:
104      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
105        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
106        with pkg/cheapaml.
107    o utils/python: add subpackage for cubed sphere function, first example is
108        simple cs.pcol to plot 2D fields on a map
109    o pkg/streamice:
110      - This is a new package in MITgcm, which solves dynamic equations for ice
111         sheets and ice streams
112      - At the moment it is independent of atmosphere/ocean dynamics, or any
113        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
114        ed that this will change)
115      - There is a new verification exercise that tests it, halfpipe_streamice,
116        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
117        rectangular embayment
118      - halfpipe_streamice is forward-only for now, will have TAF test soon
119      - for questions, email dgoldber@mit.edu
120    o pkg/thsice:
121      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
122        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
123      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
124         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
125      - allow precip from pkg/cheapaml to make snow over seaice.
126    o pkg/cfc:
127      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
128      - remove atmos CFC 2-D arrays from common bloc (now local variables)
129      - change some hard-coded constant to run time parameter for reading and
130        and interpolating atmospheric CFC ; keep same default as previously.
131      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
132      - put arguments in standard order: myTime, myIter, myThid
133      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
134        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
135      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
136      - new routine to print summary of CFC params and check for consistency.
137    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
138      similar to thsice_advdiff.
139      Note that for the B-grid case the routine parameters uc/vc are overwritten.
140    o pkg/cfc:
141      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
142        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
143      - fix interpolation of atmphspheric CFC between Sorthern and Northern
144        hemisphere value.
145    o pkg/seaice:
146      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
147    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
148                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
149      - requires an additional time level that is stored in the pickup
150      - you can start with AB2 from a pickup without this time level with
151        pickupStrictlyMatch = .false.
152    
153    checkpoint64h (2013/05/26)
154    o pkg/cheapaml:
155      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
156        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
157      - consistent treatment of uWind,vWind location: assume everywhere in
158        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
159        (Note: was already the case for Tair,Qair advection);
160        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
161      - compute diabatic forcing only in the interior (excluding overlap regions)
162      - fill in array "Qsw" (for short-wave heating);
163      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
164        before any update (consistent with MITgcm state var diagnostics);
165      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
166        non periodic ; + adjusted for uWind,vWind (C-grid).
167    o pkg/seaice:
168      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
169        add explicitly pkg/exf in experiments that currently use pkg/seaice.
170      - allows to compile pkg/seaice without pkg/exf.
171    o tools/OAD_support:
172      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
173        of array "ourStepOf" in function rvNextAction (revolve.F90).
174    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
175      - change pkg name (to be used with other atmospheric physics pkg)
176        but by-pass CVS when making the new pkg so that we keep the CVS history.
177    o pkg/offline:
178      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
179        (previously called from pkg/dic_surfforcing_init.F)
180    o model/src:
181      - re-order sequence of calls within packages_init_variables.F, using
182        standard order, except for:
183         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
184         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
185    o new pkg: atm_phys
186      - add entry point and source code (previously in contrib
187          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
188        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
189      - re-order sequence of calls within packages_readparms.F,
190         packages_init_fixed.F and packages_write_pickup.F
191        (but skip packages_init_variables.F because of TAF issues).
192      - update contrib/*/atm_gray/ experiment.
193    o pkg/seaice (ITD code):
194      - simplify and fix the writing of pickup-files for ITD case
195    o pkg/seaice (ITD code):
196      - introduce floe size dependent lateral melt for ITD case;
197      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
198      - update seaice_itd experiment main output.
199    o pkg/thsice:
200      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
201        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
202        changed accordingly pkg/atm2d.
203    
204    checkpoint64g (2013/05/01)
205    o pkg/exf ALLOW_RUNOFTEMP
206      - if defined,  river and glacier runoff temperature can be read-in from
207        runoftempfile; runoftempfile needs to have same format as runofffile
208    o pkg/thsice (& pkg/bulk_force):
209      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
210        for energy content of Precip + RunOff & Evap (like with pkg/exf).
211      - change computation domain to always be the interior (without overlap).
212      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
213    o verification/tutorial_global_oce_biogeo:
214      - add preliminary OpenAD setup (still has problems)
215    o pkg/seaice:
216      - turn some parameters for choosing the convergence criterion of
217        the inexact Newton method (JFNK) into runtime parameters for convenience
218      - clean up seaice_calc_viscosities.F: remove/retire two options for
219        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
220        the results of lab_sea/input because a division has been replaced by
221        a multiplication with the reciprocal (sumNorm)
222      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
223        convergence of solver (changes results, of course), and to test some
224        new features
225    o model/src:
226      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
227      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
228      - move forcing adjustment (balancing surface forcing) in specific S/R
229        where might also be applied exchanges (if needed) to forcing arrays.
230    o pkg/shelfice:
231      - allow to specify the Ice-Shelf mass per unit area (instead of
232        shelficeLoadAnomaly) and do the conversion from one to the other
233      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
234        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
235        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
236        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
237      - update isomip experiment forward output (get machine truncation error
238        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
239    o verification/offline_exf_seaice:
240      revise data.seaice in input.thermo and input_ad and update results accordingly
241        HO = 0.2, SEAICE_areaLossFormula = 2,
242        SEAICE_growMeltByConv = .TRUE.,
243        SEAICE_doOpenWaterMelt = .TRUE.,
244      Improve consistency with input.thsice and fix the spurious 500m ice corners
245    o verification/global_ocean.cs32x15:
246      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
247        in icedyn (thsice+seaice-dyn) test and update output.
248    o verification/offline_exf_seaice:
249      - adjust list of tested variables (with testreport) and update
250        standard test output with better slection of monitored fields.
251    o pkg/cd_code:
252      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
253        experiment lab_sea.hb87
254    o tools/genmake2:
255      - change default makedepend from the system default to tools/xmakedepend:
256        When no makedepend is specified, select tools/xmakedepend it the test pass,
257        otherwise select the system default (if exist and pass the test) or
258        try to build cyrus-makedepend ; stop if none of the 3 works.
259    o pkg/exf & pkg/thsice:
260      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
261        for energy content of Precip + RunOff & Evap. Assumes:
262       1) Rain has same temp as Air.
263       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
264       3) Run-Off comes at the temp of surface water (with same Cp)
265       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
266        put directly into Latent Heat flux & should use water-vapor heat capacity.
267       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
268        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
269    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
270        (compile when SEAICE_ALLOW_JFNK is defined)
271    o pkg/thsice:
272      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
273        implementation): move THSICE_AVE call after the advection (called directly
274        from thsice_do_advect.F).
275    o verification/global_ocean.90x40x15 and OpenAD:
276      New experiment for OpenAD is identical to the one in input_ad except that
277        multiDimAdvection=.FALSE.,
278      There is still an issue with this.
279    o pkg/thsice:
280      - account for ice velocity (ocean relative velocity) in turbulent heat flux
281        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
282        and offline_exf_seaice (main test).
283    
284    checkpoint64f (2013/03/31)
285    o verification/OpenAD:
286      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
287    o verification/isomip, pkg/shelfice and OpenAD:
288      - add OpenAD setup to this exp and make shelfice package work with OpenAD
289    o verification/tutorial_global_oce_biogeo:
290      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
291    o verification/offline_exf_seaice:
292      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
293    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
294      - add OpenAD setup to this exp and make ptracers package work with OpenAD
295    o pkg/seaice/seaice_evp.F:
296       mask the asymmetric contribution of the ice-ocean stress (when
297       the turningAngle is non-zero) over open water to avoid stripes
298       in the EVP-solutions after many EVP-substeps. This does not change
299       the verification experiment (because turningAngle=0 in that experiment),
300       but will affect other EVP solutions with turningAngle.ne.0
301    o verification, AD & TLM output:
302      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
303        additions and multiplications which affect results at machine truncation
304        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
305        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
306        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
307        digits of matching.
308    o pkg/seaice:
309       modify lsr-algorithm so that it vectorizes AND converges by using a
310       "zebra" method: split vector loop into two with step size 2; this
311       solves a general convergence problem for the JFNK solver on a vector
312       computer. It has the potential to even improve convergence for
313       non-vector machines, but it does change the results so it is turned
314       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
315       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
316    
317    checkpoint64e (2013/03/05)
318    o pkg/ecco and several verification experiments:
319       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
320       from ecco package, and revert to unified routine in model/src/
321       Adjust verification experiments accordingly, especially gloal_oce_llc90
322       Should conclude long-standing work by Gael to reconsile the_main_loop with
323       ECCO and will enable OpenAD's revolve loop in ECCO setup.
324    o pkg/generic_advdiff:
325      - implement compressible flow method for multi-dim advection (similar to
326        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
327        TAF generates many recomputations) to use it; no yet coded with implicit
328        vertical advection.
329      - change experiment advect_cs (new output) and advect_xy (same output)
330        to test compressible flow multi-dim advection.
331    o pkg/generic_advdiff:
332      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
333        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
334    o pkg/seaice:
335      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
336        bug affects two verification experiments (lab_sea and lab_sea.hb87),
337        recover old (wrong) results by setting noSlipFac = 2. in
338        seaice_calc_strainrates.F;
339      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
340      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
341        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
342      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
343    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
344      - new subroutines seaice_lsr_tridiagu/v
345      - introduce loop bounds i/jmin/max to be able to use a restricted
346        additive Schwarz method, but not used for now.
347      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
348      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
349    o OpenAD support
350       Reorganize S/R call for overall time-stepping loop to facilitate
351       OpenAD revolve loop replacement
352       (new S/R main_do_loop.F)
353    o model/src:
354      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
355      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
356        ADAMS_BASHFORTH2.
357  o pkg/cheapaml:  o pkg/cheapaml:
358    - add new parameter (default=F, same as before) to disable full domain    - add new parameter (default=F, same as before) to disable full domain
359      (including land) periodicity in X & Y dir.      (including land) periodicity in X & Y dir.

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